diff --git a/Code/BasicFilters/otbConvolutionImageFilter.txx b/Code/BasicFilters/otbConvolutionImageFilter.txx
index 94b9db348b9e67b74cf0875ef414a6c1601a6cb8..722cd0ba772988afe7b8b9a79b00fa7afe625b40 100644
--- a/Code/BasicFilters/otbConvolutionImageFilter.txx
+++ b/Code/BasicFilters/otbConvolutionImageFilter.txx
@@ -27,6 +27,8 @@
#include "itkProgressReporter.h"
#include "itkConstantBoundaryCondition.h"
+#include "otbMacro.h"
+
namespace otb
{
diff --git a/Code/Common/otbVectorDataToLabelMapFilter.txx b/Code/Common/otbVectorDataToLabelMapFilter.txx
index 5754014cc2375dcf63d766017dccc37b55093205..f5ca114a082b9e71a54b2b04b8feb1ae8e9c3bcd 100644
--- a/Code/Common/otbVectorDataToLabelMapFilter.txx
+++ b/Code/Common/otbVectorDataToLabelMapFilter.txx
@@ -312,10 +312,10 @@ VectorDataToLabelMapFilter< TVectorData, TLabelMap >
std::cout << "spacing " << this->GetOutput()->GetSpacing()<< std::endl;
// For each position in the bounding region of the polygon
- for (unsigned int i = polygonExtRingBoundReg.GetOrigin(0);i < polygonExtRingBoundReg.GetOrigin(0) + polygonExtRingBoundReg.GetSize(0) ;i+=this->GetOutput()->GetSpacing()[0])
+ for (double i = polygonExtRingBoundReg.GetOrigin(0);i < polygonExtRingBoundReg.GetOrigin(0) + polygonExtRingBoundReg.GetSize(0) ;i+=this->GetOutput()->GetSpacing()[0])
{
vertex[0] = static_cast<VertexValueType>(i) ;
- for (unsigned int j = polygonExtRingBoundReg.GetOrigin(1);j<polygonExtRingBoundReg.GetOrigin(1) + polygonExtRingBoundReg.GetSize(1) ;j+=this->GetOutput()->GetSpacing()[1])
+ for (double j = polygonExtRingBoundReg.GetOrigin(1);j<polygonExtRingBoundReg.GetOrigin(1) + polygonExtRingBoundReg.GetSize(1) ;j+=this->GetOutput()->GetSpacing()[1])
{
vertex[1] = static_cast<VertexValueType>(j) ;
diff --git a/Code/Radiometry/otbRadarFunctors.txx b/Code/Radiometry/otbRadarFunctors.txx
index 46fcf2bea0972cfbd1956dc2a499ac1e6abdd11a..f1268e7ab2e0acf6af0876359050b6403f770482 100644
--- a/Code/Radiometry/otbRadarFunctors.txx
+++ b/Code/Radiometry/otbRadarFunctors.txx
@@ -45,7 +45,7 @@ TerraSarCalibrationImageFunctor<TInput, TOutput>
m_PRF = 1.;
}
-
+
template <class TInput, class TOutput>
double
TerraSarCalibrationImageFunctor<TInput, TOutput>
@@ -63,11 +63,11 @@ TerraSarCalibrationImageFunctor<TInput, TOutput>
{
curRange = m_NoiseRangeValidityRef + ( m_NoiseRangeValidityMax-m_NoiseRangeValidityRef )/width_2 * (static_cast<double>(colId+1) - width_2 );
}
-
+
return curRange;
}
-
+
template <class TInput, class TOutput>
typename TerraSarCalibrationImageFunctor<TInput, TOutput>::DoubleVectorType
TerraSarCalibrationImageFunctor<TInput, TOutput>
@@ -75,7 +75,7 @@ TerraSarCalibrationImageFunctor<TInput, TOutput>
{
DoubleVectorType curCoeffs;
if(m_UseFastCalibrationMethod)
- {
+ {
curCoeffs = m_NoisePolynomialCoefficientsList[0];
}
else
@@ -89,7 +89,7 @@ TerraSarCalibrationImageFunctor<TInput, TOutput>
bool go = true;
// deduct the corresponding noise acquisition index
while( id<m_TimeUTC.size() && go)
- {
+ {
if( currTimeUTC < m_TimeUTC[id] )
go = false;
id++;
@@ -114,19 +114,19 @@ TerraSarCalibrationImageFunctor<TInput, TOutput>
{
double diffCurRange = ComputeCurrentNoise( static_cast<unsigned int>(index[0]) ) - m_NoiseRangeValidityRef;
DoubleVectorType curCoeff = ComputeCurrentCoeffs( static_cast<unsigned int>(index[1]) );
-
+
TOutput outRadBr = m_RadarBrightness( inPix );
double NEBN = 0.;
- for(int i=0; i<curCoeff.size(); i++)
+ for(unsigned int i=0; i<curCoeff.size(); i++)
{
NEBN += curCoeff[i]*vcl_pow( diffCurRange, i);
}
double sigma = ( outRadBr - m_CalFactor*NEBN ) * m_SinLocalIncidentAngle;
-
+
return static_cast<TOutput>(sigma);
}
-
+
/** Constructor */
template <class TInput, class TOutput>
@@ -145,7 +145,7 @@ TerraSarCalibrationComplexImageFunctor<TInput, TOutput>
m_PRF = 1.;
}
-
+
template <class TInput, class TOutput>
double
TerraSarCalibrationComplexImageFunctor<TInput, TOutput>
@@ -163,11 +163,11 @@ TerraSarCalibrationComplexImageFunctor<TInput, TOutput>
{
curRange = m_NoiseRangeValidityRef + ( m_NoiseRangeValidityMax-m_NoiseRangeValidityRef )/width_2 * (static_cast<double>(colId+1) - width_2 );
}
-
+
return curRange;
}
-
+
template <class TInput, class TOutput>
typename TerraSarCalibrationComplexImageFunctor<TInput, TOutput>::DoubleVectorType
TerraSarCalibrationComplexImageFunctor<TInput, TOutput>
@@ -175,7 +175,7 @@ TerraSarCalibrationComplexImageFunctor<TInput, TOutput>
{
DoubleVectorType curCoeffs;
if(m_UseFastCalibrationMethod)
- {
+ {
curCoeffs = m_NoisePolynomialCoefficientsList[0];
}
else
@@ -189,7 +189,7 @@ TerraSarCalibrationComplexImageFunctor<TInput, TOutput>
bool go = true;
// deduct the corresponding noise acquisition index
while( id<m_TimeUTC.size() && go)
- {
+ {
if( currTimeUTC < m_TimeUTC[id] )
go = false;
id++;
@@ -214,7 +214,7 @@ TerraSarCalibrationComplexImageFunctor<TInput, TOutput>
{
double diffCurRange = this->ComputeCurrentNoise( static_cast<unsigned int>(index[0]) ) - this->GetNoiseRangeValidityRef();
DoubleVectorType curCoeff = this->ComputeCurrentCoeffs( static_cast<unsigned int>(index[1]) );
-
+
double modulus = std::abs(inPix);
double outRadBr = static_cast<double>(m_RadarBrightness( modulus ));
@@ -224,15 +224,15 @@ TerraSarCalibrationComplexImageFunctor<TInput, TOutput>
NEBN += curCoeff[i]*vcl_pow( diffCurRange, i);
}
double sigma = ( outRadBr - this->GetCalFactor()*NEBN ) * this->GetSinLocalIncidentAngle();
-
+
double phase = std::arg(inPix);
TOutput out(sigma*vcl_cos(phase), sigma*vcl_sin(phase));
return out;
}
-
+
}// namespace Functor
-
+
} // namespace otb
#endif
diff --git a/Code/Visualization/otbImageWidgetController.cxx b/Code/Visualization/otbImageWidgetController.cxx
index 5f4e84557804b58d67ecd2a8d32d14890fe80199..259b422b72b89f997c7e7f08199ec2008c8476ee 100644
--- a/Code/Visualization/otbImageWidgetController.cxx
+++ b/Code/Visualization/otbImageWidgetController.cxx
@@ -82,7 +82,7 @@ void ImageWidgetController::HandleWidgetResize(std::string widgetId, int w, int
{
// Define an iterator on the action handlers list
ActionHandlerListType::Iterator it = m_ActionHandlersList->Begin();
-
+
// The action handler found
ActionHandlerType * handler;
@@ -93,7 +93,7 @@ void ImageWidgetController::HandleWidgetResize(std::string widgetId, int w, int
// try to handle the event with the current handler
handler->HandleWidgetResize(widgetId,w,h);
++it;
- }
+ }
}
void ImageWidgetController::HandleWidgetMove(std::string widgetId, int x, int y)
@@ -101,7 +101,7 @@ void ImageWidgetController::HandleWidgetMove(std::string widgetId, int x, int y)
otbMsgDevMacro(<<"ImageWidgetController::HandleWidgetMove(): ("<<widgetId<<", "<<x<<", "<<y<<")");
// Define an iterator on the action handlers list
ActionHandlerListType::Iterator it = m_ActionHandlersList->Begin();
-
+
// The action handler found
ActionHandlerType * handler;
@@ -118,10 +118,10 @@ void ImageWidgetController::HandleWidgetMove(std::string widgetId, int x, int y)
void ImageWidgetController::ActivateActionHandlers()
{
- otbMsgDevMacro(<<"ImageWidgetController::DectivateActionHandler(): ("<<widgetId<<")");
+// otbMsgDevMacro(<<"ImageWidgetController::DectivateActionHandler(): ("<<widgetId<<")");
// Define an iterator on the action handlers list
ActionHandlerListType::Iterator it = m_ActionHandlersList->Begin();
-
+
// The action handler found
ActionHandlerType * handler;
@@ -137,10 +137,10 @@ void ImageWidgetController::ActivateActionHandlers()
void ImageWidgetController::DeactivateActionHandlers()
{
- otbMsgDevMacro(<<"ImageWidgetController::DectivateActionHandler(): ("<<widgetId<<")");
+// otbMsgDevMacro(<<"ImageWidgetController::DectivateActionHandler(): ("<<widgetId<<")");
// Define an iterator on the action handlers list
ActionHandlerListType::Iterator it = m_ActionHandlersList->Begin();
-
+
// The action handler found
ActionHandlerType * handler;
diff --git a/Examples/OBIA/ImageToLabelToImage.cxx b/Examples/OBIA/ImageToLabelToImage.cxx
index 97144bf626c3f2df34977e39d476070728aa9959..db4fa2eaa327ae8f6e99a916b900ac6f4447f966 100644
--- a/Examples/OBIA/ImageToLabelToImage.cxx
+++ b/Examples/OBIA/ImageToLabelToImage.cxx
@@ -57,22 +57,22 @@ int main(int argc, char * argv[])
const int dim = 2;
typedef unsigned short PixelType;
-
+
typedef otb::Image< PixelType, dim > ImageType;
typedef itk::LabelObject< PixelType, dim > LabelObjectType;
typedef itk::LabelMap< LabelObjectType > LabelMapType;
-
+
typedef itk::ImageFileReader< ImageType > ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName( argv[1] );
-
+
typedef itk::BinaryImageToLabelMapFilter< ImageType, LabelMapType> I2LType;
I2LType::Pointer i2l = I2LType::New();
i2l->SetInput( reader->GetOutput() );
i2l->SetFullyConnected( atoi(argv[5]) );
- i2l->SetForegroundValue( atoi(argv[6]) );
- i2l->SetBackgroundValue( atoi(argv[7]) );
+ i2l->SetInputForegroundValue( atoi(argv[6]) );
+ i2l->SetOutputBackgroundValue( atoi(argv[7]) );
typedef itk::LabelMapToLabelImageFilter< LabelMapType, ImageType> L2IType;
L2IType::Pointer l2i = L2IType::New();
diff --git a/Utilities/ITK/Code/Review/itkBinaryImageToLabelMapFilter.h b/Utilities/ITK/Code/Review/itkBinaryImageToLabelMapFilter.h
index 8835e6d8cf208bbc81923c9248a67ca31e21010f..be772383adf95d1538e1e05b05938fbe5120e620 100644
--- a/Utilities/ITK/Code/Review/itkBinaryImageToLabelMapFilter.h
+++ b/Utilities/ITK/Code/Review/itkBinaryImageToLabelMapFilter.h
@@ -26,6 +26,9 @@
#include "itkProgressReporter.h"
#include "itkBarrier.h"
+//PATCH OTB
+#include "itkLabelMap.h"
+
namespace itk
{
diff --git a/Utilities/InsightJournal/itkAutoCropLabelMapFilter.h b/Utilities/InsightJournal/itkAutoCropLabelMapFilter.h
deleted file mode 100644
index c7ff8acba30e8488ea3e306d565cb87402c68ae8..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkAutoCropLabelMapFilter.h
+++ /dev/null
@@ -1,114 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkAutoCropLabelMapFilter.h,v $
- Language: C++
- Date: $Date: 2004/07/11 14:56:38 $
- 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.
-
- Portions of this code are covered under the VTK copyright.
- See VTKCopyright.txt or http://www.kitware.com/VTKCopyright.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 __itkAutoCropLabelMapFilter_h
-#define __itkAutoCropLabelMapFilter_h
-
-#include "itkChangeRegionLabelMapFilter.h"
-
-namespace itk
-{
-
-/** \class AutoCropLabelMapFilter
- * \brief Crop a LabelMap image to fit exactly the objects in the LabelMap
- *
- * The CropBorder can be used to add a border which will never be larger than
- * the input image. To add a border of size independant of the input image,
- * PadLabelMapFilter can be used.
- *
- * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
- *
- * \sa PadLabelMapFilter
- * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
- */
-template <class TInputImage>
-class ITK_EXPORT AutoCropLabelMapFilter : public ChangeRegionLabelMapFilter<TInputImage>
-{
-public:
- /** Standard class typedefs. */
- typedef AutoCropLabelMapFilter Self;
- typedef ChangeRegionLabelMapFilter<TInputImage> Superclass;
- typedef SmartPointer<Self> Pointer;
- typedef SmartPointer<const Self> ConstPointer;
-
-
- /** Run-time type information (and related methods). */
- itkTypeMacro(AutoCropLabelMapFilter, ChangeRegionImageFilter);
-
- /** Standard New method. */
- itkNewMacro(Self);
-
- /** Superclass typedefs. */
- typedef typename Superclass::OutputImageType OutputImageType;
- typedef typename Superclass::OutputImagePointer OutputImagePointer;
- typedef typename Superclass::OutputImageRegionType OutputImageRegionType;
- typedef typename Superclass::OutputImagePixelType OutputImagePixelType;
-
- /** 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 InputImageType::PixelType PixelType;
- typedef typename InputImageType::IndexType IndexType;
- typedef typename InputImageType::SizeType SizeType;
- typedef typename InputImageType::RegionType RegionType;
-
- typedef TInputImage TOutputImage;
-
- /** ImageDimension constants */
- itkStaticConstMacro(InputImageDimension, unsigned int,
- TInputImage::ImageDimension);
- itkStaticConstMacro(OutputImageDimension, unsigned int,
- TOutputImage::ImageDimension);
- itkStaticConstMacro(ImageDimension, unsigned int,
- TOutputImage::ImageDimension);
-
-
- /**
- * 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:
- AutoCropLabelMapFilter();
- ~AutoCropLabelMapFilter() {};
-
- virtual void GenerateOutputInformation();
-
-private:
- AutoCropLabelMapFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
- SizeType m_CropBorder;
- TimeStamp m_CropTimeStamp;
-
-};
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkAutoCropLabelMapFilter.txx"
-#endif
-
-#endif
diff --git a/Utilities/InsightJournal/itkAutoCropLabelMapFilter.txx b/Utilities/InsightJournal/itkAutoCropLabelMapFilter.txx
deleted file mode 100644
index eec12a54ba96d226ddff561c87848e81f8f60489..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkAutoCropLabelMapFilter.txx
+++ /dev/null
@@ -1,136 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkAutoCropLabelMapFilter.txx,v $
- Language: C++
- Date: $Date: 2004/07/11 14:56:39 $
- 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.
-
- Portions of this code are covered under the VTK copyright.
- See VTKCopyright.txt or http://www.kitware.com/VTKCopyright.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 _itkAutoCropLabelMapFilter_txx
-#define _itkAutoCropLabelMapFilter_txx
-#include "itkAutoCropLabelMapFilter.h"
-
-
-namespace itk
-{
-
-template <class TInputImage>
-AutoCropLabelMapFilter<TInputImage>
-::AutoCropLabelMapFilter()
-{
- m_CropBorder.Fill( 0 );
-}
-
-
-template <class TInputImage>
-void
-AutoCropLabelMapFilter<TInputImage>
-::GenerateOutputInformation()
-{
-
- 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;
- }
-
- // 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();
-
- // just find the bounding box of the objects
- IndexType mins;
- mins.Fill( NumericTraits< long >::max() );
- IndexType maxs;
- maxs.Fill( NumericTraits< long >::NonpositiveMin() );
- // iterate over all the lines
- typename InputImageType::LabelObjectContainerType container = this->GetInput()->GetLabelObjectContainer();
- for( typename InputImageType::LabelObjectContainerType::const_iterator loit = container.begin();
- loit != container.end();
- loit++ )
- {
- const LabelObjectType * labelObject = loit->second;
- typename LabelObjectType::LineContainerType::const_iterator lit;
- const typename LabelObjectType::LineContainerType & lineContainer = labelObject->GetLineContainer();
- 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->SetRegion(cropRegion);
- m_CropTimeStamp.Modified();
-
- 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;
-}
-
-
-} // end namespace itk
-
-#endif
diff --git a/Utilities/InsightJournal/itkBinaryImageToLabelMapFilter.h b/Utilities/InsightJournal/itkBinaryImageToLabelMapFilter.h
deleted file mode 100644
index f236770f27138c3f1f70c8d96417fc61bc605d6d..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkBinaryImageToLabelMapFilter.h
+++ /dev/null
@@ -1,256 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkBinaryImageToLabelMapFilter.h,v $
- Language: C++
- Date: $Date: 2007/02/18 20:03:03 $
- Version: $Revision: 1.16 $
-
- 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 __itkBinaryImageToLabelMapFilter_h
-#define __itkBinaryImageToLabelMapFilter_h
-
-#include "itkLabelMap.h"
-#include "itkLabelObject.h"
-#include "itkImageToImageFilter.h"
-#include "itkImage.h"
-#include "itkConceptChecking.h"
-#include <vector>
-#include <map>
-#include "itkProgressReporter.h"
-#include "itkBarrier.h"
-
-namespace itk
-{
-
-/**
- * \class BinaryImageToLabelMapFilter
- * \brief Label the connected components in a binary image and produce a collection of label objects
- *
- * BinaryImageToLabelMapFilter labels the objects in a binary image.
- * Each distinct object is assigned a unique label.
- * The final object labels start with 1 and are consecutive. Objects
- * that are reached earlier by a raster order scan have a lower
- * label.
- *
- * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
- *
- * \sa ConnectedComponentImageFilter, LabelImageToLabelMapFilter, LabelMap
- */
-
-template <class TInputImage, class TOutputImage=LabelMap< LabelObject< unsigned long, TInputImage::ImageDimension > > >
-class ITK_EXPORT BinaryImageToLabelMapFilter :
- public ImageToImageFilter< TInputImage, TOutputImage >
-{
-public:
- /**
- * Standard "Self" & Superclass typedef.
- */
- typedef BinaryImageToLabelMapFilter Self;
- typedef ImageToImageFilter< TInputImage, TOutputImage > Superclass;
-
- /**
- * Types from the Superclass
- */
- typedef typename Superclass::InputImagePointer InputImagePointer;
-
- /**
- * Extract some information from the image types. Dimensionality
- * of the two images is assumed to be the same.
- */
- typedef typename TOutputImage::PixelType OutputPixelType;
- typedef typename TInputImage::PixelType InputPixelType;
- itkStaticConstMacro(ImageDimension, unsigned int,
- TOutputImage::ImageDimension);
- itkStaticConstMacro(OutputImageDimension, unsigned int,
- TOutputImage::ImageDimension);
- itkStaticConstMacro(InputImageDimension, unsigned int,
- TInputImage::ImageDimension);
-
- /**
- * Image typedef support
- */
- typedef TInputImage InputImageType;
- typedef typename TInputImage::IndexType IndexType;
- typedef typename TInputImage::SizeType SizeType;
- typedef typename TInputImage::OffsetType OffsetType;
-
- typedef TOutputImage OutputImageType;
- typedef typename TOutputImage::RegionType RegionType;
- typedef typename TOutputImage::IndexType OutputIndexType;
- typedef typename TOutputImage::SizeType OutputSizeType;
- typedef typename TOutputImage::OffsetType OutputOffsetType;
- typedef typename TOutputImage::PixelType OutputImagePixelType;
-
- typedef std::list<IndexType> ListType;
-
- /**
- * Smart pointer typedef support
- */
- typedef SmartPointer<Self> Pointer;
- typedef SmartPointer<const Self> ConstPointer;
-
- /**
- * Run-time type information (and related methods)
- */
- itkTypeMacro(BinaryImageToLabelMapFilter, ImageToImageFilter);
-
- /**
- * Method for creation through the object factory.
- */
- itkNewMacro(Self);
-
- /**
- * 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);
-
- // only set after completion
- itkGetConstReferenceMacro(ObjectCount, unsigned long);
-
- // Concept checking -- input and output dimensions must be the same
- itkConceptMacro(SameDimension,
- (Concept::SameDimension<itkGetStaticConstMacro(InputImageDimension),
- itkGetStaticConstMacro(OutputImageDimension)>));
-
-
- /**
- * Set/Get the value used as "background" in the output image.
- * Defaults to NumericTraits<PixelType>::NonpositiveMin().
- */
- itkSetMacro(BackgroundValue, OutputPixelType);
- itkGetConstMacro(BackgroundValue, OutputPixelType);
-
- /**
- * Set/Get the value used as "foreground" in the output image.
- * Defaults to NumericTraits<PixelType>::max().
- */
- itkSetMacro(ForegroundValue, InputPixelType);
- itkGetConstMacro(ForegroundValue, InputPixelType);
-
-protected:
- BinaryImageToLabelMapFilter()
- {
- m_FullyConnected = false;
- m_ObjectCount = 0;
- m_BackgroundValue = NumericTraits<OutputPixelType>::NonpositiveMin();
- m_ForegroundValue = NumericTraits<InputPixelType>::max();
- }
- virtual ~BinaryImageToLabelMapFilter() {}
- void PrintSelf(std::ostream& os, Indent indent) const;
-
- /**
- * Standard pipeline method.
- */
- void BeforeThreadedGenerateData ();
- void AfterThreadedGenerateData ();
- void ThreadedGenerateData (const RegionType& outputRegionForThread, int threadId) ;
-
- /** BinaryImageToLabelMapFilter needs the entire input. Therefore
- * it must provide an implementation GenerateInputRequestedRegion().
- * \sa ProcessObject::GenerateInputRequestedRegion(). */
- void GenerateInputRequestedRegion();
-
- /** BinaryImageToLabelMapFilter will produce all of the output.
- * Therefore it must provide an implementation of
- * EnlargeOutputRequestedRegion().
- * \sa ProcessObject::EnlargeOutputRequestedRegion() */
- void EnlargeOutputRequestedRegion(DataObject *itkNotUsed(output));
-
- bool m_FullyConnected;
-
-private:
- BinaryImageToLabelMapFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
- OutputPixelType m_BackgroundValue;
- InputPixelType m_ForegroundValue;
-
- unsigned long m_ObjectCount;
- // some additional types
- typedef typename TOutputImage::RegionType::SizeType OutSizeType;
-
- // types to support the run length encoding of lines
- class runLength
- {
- public:
- // run length information - may be a more type safe way of doing this
- long int length;
- typename InputImageType::IndexType where; // Index of the start of the run
- unsigned long int label; // the initial label of the run
- };
-
- typedef std::vector<runLength> lineEncoding;
-
- // the map storing lines
- typedef std::vector<lineEncoding> LineMapType;
-
- typedef std::vector<long> OffsetVec;
-
- // the types to support union-find operations
- typedef std::vector<unsigned long int> UnionFindType;
- UnionFindType m_UnionFind;
- UnionFindType m_Consecutive;
- // functions to support union-find operations
- void InitUnion(const unsigned long int size)
- {
- m_UnionFind = UnionFindType(size + 1);
- }
- void InsertSet(const unsigned long int label);
- unsigned long int LookupSet(const unsigned long int label);
- void LinkLabels(const unsigned long int lab1, const unsigned long int lab2);
- unsigned long int CreateConsecutive();
- //////////////////
- bool CheckNeighbors(const OutputIndexType &A,
- const OutputIndexType &B);
-
- void CompareLines(lineEncoding ¤t, const lineEncoding &Neighbour);
-
- void FillOutput(const LineMapType &LineMap,
- ProgressReporter &progress);
-
- void SetupLineOffsets(OffsetVec &LineOffsets);
-
- void Wait()
- {
- long nbOfThreads = this->GetNumberOfThreads();
- if( itk::MultiThreader::GetGlobalMaximumNumberOfThreads() != 0 )
- {
- nbOfThreads = std::min( this->GetNumberOfThreads(), itk::MultiThreader::GetGlobalMaximumNumberOfThreads() );
- }
- if( nbOfThreads > 1 )
- {
- m_Barrier->Wait();
- }
- }
-
- typename std::vector< long > m_NumberOfLabels;
- typename std::vector< long > m_FirstLineIdToJoin;
- typename Barrier::Pointer m_Barrier;
-#if !defined(CABLE_CONFIGURATION)
- LineMapType m_LineMap;
-#endif
-};
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#if !defined(CABLE_CONFIGURATION)
-#include "itkBinaryImageToLabelMapFilter.txx"
-#endif
-#endif
-
-#endif
diff --git a/Utilities/InsightJournal/itkBinaryImageToLabelMapFilter.txx b/Utilities/InsightJournal/itkBinaryImageToLabelMapFilter.txx
deleted file mode 100644
index dedc98013f773494014563d64e0a92ac39689cc0..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkBinaryImageToLabelMapFilter.txx
+++ /dev/null
@@ -1,615 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkBinaryImageToLabelMapFilter.txx,v $
- Language: C++
- Date: $Date: 2007/02/20 15:28:29 $
- Version: $Revision: 1.21 $
-
- 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 __itkBinaryImageToLabelMapFilter_txx
-#define __itkBinaryImageToLabelMapFilter_txx
-
-#include "itkBinaryImageToLabelMapFilter.h"
-#include "itkNumericTraits.h"
-
-// don't think we need the indexed version as we only compute the
-// index at the start of each run, but there isn't a choice
-#include "itkImageLinearConstIteratorWithIndex.h"
-#include "itkConstShapedNeighborhoodIterator.h"
-#include "itkImageRegionIterator.h"
-#include "itkConnectedComponentAlgorithm.h"
-
-namespace itk
-{
-template< class TInputImage, class TOutputImage >
-void
-BinaryImageToLabelMapFilter< 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
-BinaryImageToLabelMapFilter< TInputImage, TOutputImage>
-::EnlargeOutputRequestedRegion(DataObject *)
-{
- this->GetOutput()
- ->SetRequestedRegion( this->GetOutput()->GetLargestPossibleRegion() );
-}
-
-
-template< class TInputImage, class TOutputImage >
-void
-BinaryImageToLabelMapFilter< TInputImage, TOutputImage >
-::BeforeThreadedGenerateData()
-{
- typename TOutputImage::Pointer output = this->GetOutput();
- typename TInputImage::ConstPointer input = this->GetInput();
-
- output->SetBackgroundValue( m_BackgroundValue );
-
- long nbOfThreads = this->GetNumberOfThreads();
- if( itk::MultiThreader::GetGlobalMaximumNumberOfThreads() != 0 )
- {
- nbOfThreads = std::min( this->GetNumberOfThreads(), itk::MultiThreader::GetGlobalMaximumNumberOfThreads() );
- }
- // number of threads can be constrained by the region size, so call the SplitRequestedRegion
- // to get the real number of threads which will be used
- typename TOutputImage::RegionType splitRegion; // dummy region - just to call the following method
- nbOfThreads = this->SplitRequestedRegion(0, nbOfThreads, splitRegion);
- // std::cout << "nbOfThreads: " << nbOfThreads << std::endl;
-
- // set up the vars used in the threads
- m_NumberOfLabels.clear();
- m_NumberOfLabels.resize( nbOfThreads, 0 );
- m_Barrier = Barrier::New();
- m_Barrier->Initialize( nbOfThreads );
- long pixelcount = output->GetRequestedRegion().GetNumberOfPixels();
- long xsize = output->GetRequestedRegion().GetSize()[0];
- long linecount = pixelcount/xsize;
- m_LineMap.resize( linecount );
- m_FirstLineIdToJoin.resize( nbOfThreads - 1 );
-}
-
-
-template< class TInputImage, class TOutputImage >
-void
-BinaryImageToLabelMapFilter< TInputImage, TOutputImage >
-::ThreadedGenerateData(const RegionType& outputRegionForThread,
- int threadId)
-{
- typename TOutputImage::Pointer output = this->GetOutput();
- typename TInputImage::ConstPointer input = this->GetInput();
-
- long nbOfThreads = this->GetNumberOfThreads();
- if( itk::MultiThreader::GetGlobalMaximumNumberOfThreads() != 0 )
- {
- nbOfThreads = std::min( this->GetNumberOfThreads(), itk::MultiThreader::GetGlobalMaximumNumberOfThreads() );
- }
-
- // create a line iterator
- typedef itk::ImageLinearConstIteratorWithIndex<InputImageType>
- InputLineIteratorType;
- InputLineIteratorType inLineIt(input, outputRegionForThread);
- inLineIt.SetDirection(0);
-
- // set the progress reporter to deal with the number of lines
- long pixelcountForThread = outputRegionForThread.GetNumberOfPixels();
- long xsizeForThread = outputRegionForThread.GetSize()[0];
- long linecountForThread = pixelcountForThread/xsizeForThread;
- ProgressReporter progress(this, threadId, linecountForThread);
-
- // find the split axis
- IndexType outputRegionIdx = output->GetRequestedRegion().GetIndex();
- IndexType outputRegionForThreadIdx = outputRegionForThread.GetIndex();
- int splitAxis = 0;
- for( int i=0; i<ImageDimension; i++ )
- {
- if( outputRegionIdx[i] != outputRegionForThreadIdx[i] )
- {
- splitAxis = i;
- }
- }
-
- // compute the number of pixels before that threads
- SizeType outputRegionSize = output->GetRequestedRegion().GetSize();
- outputRegionSize[splitAxis] = outputRegionForThreadIdx[splitAxis] - outputRegionIdx[splitAxis];
- long firstLineIdForThread = RegionType( outputRegionIdx, outputRegionSize ).GetNumberOfPixels() / xsizeForThread;
- long lineId = firstLineIdForThread;
-
- OffsetVec LineOffsets;
- SetupLineOffsets(LineOffsets);
-
- long nbOfLabels = 0;
- for( inLineIt.GoToBegin();
- !inLineIt.IsAtEnd();
- inLineIt.NextLine() )
- {
- inLineIt.GoToBeginOfLine();
- lineEncoding ThisLine;
- while (! inLineIt.IsAtEndOfLine())
- {
- InputPixelType PVal = inLineIt.Get();
- //std::cout << inLineIt.GetIndex() << std::endl;
- if (PVal == m_ForegroundValue)
- {
- // We've hit the start of a run
- runLength thisRun;
- long length=0;
- IndexType thisIndex;
- thisIndex = inLineIt.GetIndex();
- //std::cout << thisIndex << std::endl;
- ++length;
- ++inLineIt;
- while( !inLineIt.IsAtEndOfLine()
- && inLineIt.Get() == m_ForegroundValue )
- {
- ++length;
- ++inLineIt;
- }
- // create the run length object to go in the vector
- thisRun.length=length;
- thisRun.label=0; // will give a real label later
- thisRun.where = thisIndex;
- ThisLine.push_back(thisRun);
- nbOfLabels++;
- }
- else
- {
- ++inLineIt;
- }
- }
- m_LineMap[lineId] = ThisLine;
- lineId++;
- progress.CompletedPixel();
- }
-
- m_NumberOfLabels[threadId] = nbOfLabels;
-
- // wait for the other threads to complete that part
- this->Wait();
-
- // compute the total number of labels
- nbOfLabels = 0;
- for( int i=0; i<nbOfThreads; i++ )
- {
- nbOfLabels += m_NumberOfLabels[i];
- }
-
- if( threadId == 0 )
- {
- // set up the union find structure
- InitUnion(nbOfLabels);
- // insert all the labels into the structure -- an extra loop but
- // saves complicating the ones that come later
- typename LineMapType::iterator MapBegin, MapEnd, LineIt;
- MapBegin = m_LineMap.begin();
- MapEnd = m_LineMap.end();
- LineIt = MapBegin;
- unsigned long label = 1;
- for (LineIt = MapBegin; LineIt != MapEnd; ++LineIt)
- {
- typename lineEncoding::iterator cIt;
- for (cIt = LineIt->begin();cIt != LineIt->end();++cIt)
- {
- cIt->label = label;
- InsertSet(label);
- label++;
- }
- }
- }
-
- // wait for the other threads to complete that part
- this->Wait();
-
- // now process the map and make appropriate entries in an equivalence
- // table
- // assert( linecount == m_LineMap.size() );
- long pixelcount = output->GetRequestedRegion().GetNumberOfPixels();
- long xsize = output->GetRequestedRegion().GetSize()[0];
- long linecount = pixelcount/xsize;
-
- long lastLineIdForThread = linecount;
- long nbOfLineIdToJoin = 0;
- if( threadId != nbOfThreads - 1 )
- {
- SizeType outputRegionForThreadSize = outputRegionForThread.GetSize();
- outputRegionForThreadSize[splitAxis] -= 1;
- lastLineIdForThread = firstLineIdForThread + RegionType( outputRegionIdx, outputRegionForThreadSize ).GetNumberOfPixels() / xsizeForThread;
- m_FirstLineIdToJoin[threadId] = lastLineIdForThread;
- // found the number of line ids to join
- nbOfLineIdToJoin = RegionType( outputRegionIdx, outputRegionForThread.GetSize() ).GetNumberOfPixels() / xsizeForThread - RegionType( outputRegionIdx, outputRegionForThreadSize ).GetNumberOfPixels() / xsizeForThread;
- }
-
- for(long ThisIdx = firstLineIdForThread; ThisIdx < lastLineIdForThread; ++ThisIdx)
- {
- if( !m_LineMap[ThisIdx].empty() )
- {
- for (OffsetVec::const_iterator I = LineOffsets.begin();
- I != LineOffsets.end(); ++I)
- {
- long NeighIdx = ThisIdx + (*I);
- // check if the neighbor is in the map
- if ( NeighIdx >= 0 && NeighIdx < linecount && !m_LineMap[NeighIdx].empty() )
- {
- // Now check whether they are really neighbors
- bool areNeighbors
- = CheckNeighbors(m_LineMap[ThisIdx][0].where, m_LineMap[NeighIdx][0].where);
- if (areNeighbors)
- {
- // Compare the two lines
- CompareLines(m_LineMap[ThisIdx], m_LineMap[NeighIdx]);
- }
- }
- }
- }
- }
-
- // wait for the other threads to complete that part
- this->Wait();
-
- while( m_FirstLineIdToJoin.size() != 0 )
- {
- if( threadId * 2 < (long)m_FirstLineIdToJoin.size() )
- {
- for(long ThisIdx = m_FirstLineIdToJoin[threadId * 2];
- ThisIdx < m_FirstLineIdToJoin[threadId * 2] + nbOfLineIdToJoin;
- ++ThisIdx)
- {
- if( !m_LineMap[ThisIdx].empty() )
- {
- for (OffsetVec::const_iterator I = LineOffsets.begin();
- I != LineOffsets.end(); ++I)
- {
- long NeighIdx = ThisIdx + (*I);
- // check if the neighbor is in the map
- if ( NeighIdx >= 0 && NeighIdx < linecount && !m_LineMap[NeighIdx].empty() )
- {
- // Now check whether they are really neighbors
- bool areNeighbors
- = CheckNeighbors(m_LineMap[ThisIdx][0].where, m_LineMap[NeighIdx][0].where);
- if (areNeighbors)
- {
- // Compare the two lines
- CompareLines(m_LineMap[ThisIdx], m_LineMap[NeighIdx]);
- }
- }
- }
- }
- }
- }
-
- this->Wait();
-
- if( threadId == 0 )
- {
- // remove the region already joined
- typename std::vector< long > newFirstLineIdToJoin;
- for( int i = 1; i<(long)m_FirstLineIdToJoin.size(); i+=2 )
- {
- newFirstLineIdToJoin.push_back( m_FirstLineIdToJoin[i] );
- }
- m_FirstLineIdToJoin = newFirstLineIdToJoin;
- }
-
- this->Wait();
-
- }
-
-}
-
-template< class TInputImage, class TOutputImage >
-void
-BinaryImageToLabelMapFilter< TInputImage, TOutputImage >
-::AfterThreadedGenerateData()
-{
- typename TOutputImage::Pointer output = this->GetOutput();
- typename TInputImage::ConstPointer input = this->GetInput();
- long pixelcount = output->GetRequestedRegion().GetNumberOfPixels();
- long xsize = output->GetRequestedRegion().GetSize()[0];
- long linecount = pixelcount/xsize;
- unsigned long int totalLabs = CreateConsecutive();
- m_ObjectCount = totalLabs;
- ProgressReporter progress(this, 0, linecount);
- // check for overflow exception here
- if( totalLabs > static_cast<unsigned long int>(
- NumericTraits<OutputPixelType>::max() ) )
- {
- itkExceptionMacro(
- << "Number of objects greater than maximum of output pixel type " );
- }
-
- for (long ThisIdx = 0; ThisIdx<linecount; ThisIdx++)
- {
- // now fill the labelled sections
- typename lineEncoding::const_iterator cIt;
-
- for (cIt = m_LineMap[ThisIdx].begin();cIt != m_LineMap[ThisIdx].end();++cIt)
- {
- unsigned long Ilab = LookupSet( cIt->label);
- OutputPixelType lab = m_Consecutive[Ilab];
- output->SetLine( cIt->where, cIt->length, lab );
-// std::cout << cIt->where << " " << cIt->length << " " << lab+0.0 << std::endl;
- }
- progress.CompletedPixel();
- }
-
- m_NumberOfLabels.clear();
- m_Barrier = NULL;
- m_LineMap.clear();
-}
-
-
-template< class TInputImage, class TOutputImage >
-void
-BinaryImageToLabelMapFilter< TInputImage, TOutputImage >
-::SetupLineOffsets(OffsetVec &LineOffsets)
-{
- // Create a neighborhood so that we can generate a table of offsets
- // to "previous" line indexes
- // We are going to mis-use the neighborhood iterators to compute the
- // offset for us. All this messing around produces an array of
- // offsets that will be used to index the map
- typename TOutputImage::Pointer output = this->GetOutput();
- typedef Image<long, TOutputImage::ImageDimension - 1> PretendImageType;
- typedef typename PretendImageType::RegionType::SizeType PretendSizeType;
- typedef typename PretendImageType::RegionType::IndexType PretendIndexType;
- typedef ConstShapedNeighborhoodIterator<PretendImageType>
- LineNeighborhoodType;
-
- typename PretendImageType::Pointer fakeImage;
- fakeImage = PretendImageType::New();
-
- typename PretendImageType::RegionType LineRegion;
- //LineRegion = PretendImageType::RegionType::New();
-
- OutSizeType OutSize = output->GetRequestedRegion().GetSize();
-
- PretendSizeType PretendSize;
- // The first dimension has been collapsed
- for (unsigned int i = 0; i<PretendSize.GetSizeDimension(); i++)
- {
- PretendSize[i] = OutSize[i+1];
- }
-
- LineRegion.SetSize(PretendSize);
- fakeImage->SetRegions( LineRegion );
- PretendSizeType kernelRadius;
- kernelRadius.Fill(1);
- LineNeighborhoodType lnit(kernelRadius, fakeImage, LineRegion);
-
- // only activate the indices that are "previous" to the current
- // pixel and face connected (exclude the center pixel from the
- // neighborhood)
- //
- setConnectivityPrevious( &lnit, m_FullyConnected );
-
- typename LineNeighborhoodType::IndexListType ActiveIndexes;
- ActiveIndexes = lnit.GetActiveIndexList();
-
- typename LineNeighborhoodType::IndexListType::const_iterator LI;
-
- PretendIndexType idx = LineRegion.GetIndex();
- long offset = fakeImage->ComputeOffset( idx );
-
- for (LI=ActiveIndexes.begin(); LI != ActiveIndexes.end(); LI++)
- {
- LineOffsets.push_back( fakeImage->ComputeOffset( idx + lnit.GetOffset( *LI ) ) - offset );
- }
-
- // LineOffsets is the thing we wanted.
-}
-
-
-template< class TInputImage, class TOutputImage >
-bool
-BinaryImageToLabelMapFilter< TInputImage, TOutputImage >
-::CheckNeighbors(const OutputIndexType &A,
- const OutputIndexType &B)
-{
- // this checks whether the line encodings are really neighbors. The
- // first dimension gets ignored because the encodings are along that
- // axis
- OutputOffsetType Off = A - B;
- for (unsigned i = 1; i < OutputImageDimension; i++)
- {
- if (abs(Off[i]) > 1)
- {
- return(false);
- }
- }
- return(true);
-}
-
-
-template< class TInputImage, class TOutputImage >
-void
-BinaryImageToLabelMapFilter< TInputImage, TOutputImage >
-::CompareLines(lineEncoding ¤t, const lineEncoding &Neighbour)
-{
- long offset = 0;
- if (m_FullyConnected)
- {
- offset = 1;
- }
-
- typename lineEncoding::const_iterator nIt, mIt;
- typename lineEncoding::iterator cIt;
-
- mIt = Neighbour.begin(); // out marker iterator
-
- for (cIt = current.begin();cIt != current.end();++cIt)
- {
- //runLength cL = *cIt;
- long cStart = cIt->where[0]; // the start x position
- long cLast = cStart + cIt->length - 1;
-
- for (nIt=mIt; nIt != Neighbour.end(); ++nIt)
- {
- //runLength nL = *nIt;
- long nStart = nIt->where[0];
- long nLast = nStart + nIt->length - 1;
- // there are a few ways that neighbouring lines might overlap
- // neighbor S E
- // current S E
- //------------------------------------------
- // neighbor S E
- // current S E
- //------------------------------------------
- // neighbor S E
- // current S E
- //------------------------------------------
- // neighbor S E
- // current S E
- //------------------------------------------
- long ss1 = nStart - offset;
- // long ss2 = nStart + offset;
- long ee1 = nLast - offset;
- long ee2 = nLast + offset;
- bool eq = false;
- // the logic here can probably be improved a lot
- if ((ss1 >= cStart) && (ee2 <= cLast))
- {
- // case 1
- eq = true;
- }
- else
- {
- if ((ss1 <= cLast) && (ee2 >= cLast))
- {
- // case 2
- eq = true;
- }
- else
- {
- if ((ss1 <= cStart) && (ee2 >= cStart))
- {
- // case 3
- eq = true;
- }
- else
- {
- if ((ss1 <= cStart) && (ee2 >= cLast))
- {
- // case 4
- eq = true;
- }
- }
- }
- }
- if (eq)
- {
- LinkLabels(nIt->label, cIt->label);
- }
-
- if (ee1 >= cLast)
- {
- // No point looking for more overlaps with the current run
- // because the neighbor run is either case 2 or 4
- mIt = nIt;
- break;
- }
- }
- }
-
-}
-
-// union find related functions
-template< class TInputImage, class TOutputImage >
-void
-BinaryImageToLabelMapFilter< TInputImage, TOutputImage >
-::InsertSet(const unsigned long int label)
-{
- m_UnionFind[label]=label;
-}
-
-template< class TInputImage, class TOutputImage >
-unsigned long int
-BinaryImageToLabelMapFilter< TInputImage, TOutputImage >
-::CreateConsecutive()
-{
- m_Consecutive = UnionFindType(m_UnionFind.size());
- m_Consecutive[m_BackgroundValue] = m_BackgroundValue;
- unsigned long int CLab = 0;
- for (unsigned long int I = 1; I < m_UnionFind.size(); I++)
- {
- unsigned long int L = m_UnionFind[I];
- if (L == I)
- {
- if( CLab == m_BackgroundValue )
- {
- ++CLab;
- }
- m_Consecutive[L] = CLab;
- ++CLab;
- }
- }
- return(CLab);
-}
-
-template< class TInputImage, class TOutputImage >
-unsigned long int
-BinaryImageToLabelMapFilter< TInputImage, TOutputImage >
-::LookupSet(const unsigned long int label)
-{
- // recursively set the equivalence if necessary
- if (label != m_UnionFind[label])
- {
- m_UnionFind[label] = this->LookupSet(m_UnionFind[label]);
- }
- return(m_UnionFind[label]);
-}
-
-template< class TInputImage, class TOutputImage >
-void
-BinaryImageToLabelMapFilter< TInputImage, TOutputImage >
-::LinkLabels(const unsigned long int lab1, const unsigned long int lab2)
-{
- unsigned long E1 = this->LookupSet(lab1);
- unsigned long E2 = this->LookupSet(lab2);
-
- if (E1 < E2)
- {
- m_UnionFind[E2] = E1;
- }
- else
- {
- m_UnionFind[E1] = E2;
- }
-
-}
-
-template< class TInputImage, class TOutputImage >
-void
-BinaryImageToLabelMapFilter< TInputImage, TOutputImage >
-::PrintSelf(std::ostream& os, Indent indent) const
-{
- Superclass::PrintSelf(os,indent);
-
- os << indent << "FullyConnected: " << m_FullyConnected << std::endl;
- os << indent << "ObjectCount: " << m_ObjectCount << std::endl;
- os << indent << "ForegroundValue: " << static_cast<typename NumericTraits<InputPixelType>::PrintType>(m_ForegroundValue) << std::endl;
- os << indent << "BackgroundValue: " << static_cast<typename NumericTraits<OutputImagePixelType>::PrintType>(m_BackgroundValue) << std::endl;
-}
-
-} // end namespace itk
-
-#endif
diff --git a/Utilities/InsightJournal/itkBinaryImageToShapeLabelMapFilter.h b/Utilities/InsightJournal/itkBinaryImageToShapeLabelMapFilter.h
deleted file mode 100644
index 9917bb7de65bec62d6d361b0c2390014e2b677e1..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkBinaryImageToShapeLabelMapFilter.h
+++ /dev/null
@@ -1,171 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkBinaryImageToShapeLabelMapFilter.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 __itkBinaryImageToShapeLabelMapFilter_h
-#define __itkBinaryImageToShapeLabelMapFilter_h
-
-#include "itkImageToImageFilter.h"
-#include "itkShapeLabelObject.h"
-#include "itkLabelMap.h"
-#include "itkBinaryImageToLabelMapFilter.h"
-#include "itkShapeLabelMapFilter.h"
-
-
-namespace itk {
-
-/** \class BinaryImageToShapeLabelMapFilter
- * \brief a convenient class to convert a binary image to a label map and valuate the shape attributes at once
- *
- * \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 TOutputImage=LabelMap< ShapeLabelObject< unsigned long, TInputImage::ImageDimension > > >
-class ITK_EXPORT BinaryImageToShapeLabelMapFilter :
- public ImageToImageFilter<TInputImage, TOutputImage>
-{
-public:
- /** Standard class typedefs. */
- typedef BinaryImageToShapeLabelMapFilter Self;
- typedef ImageToImageFilter<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 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::LabelObjectType LabelObjectType;
-
- /** ImageDimension constants */
- itkStaticConstMacro(InputImageDimension, unsigned int,
- TInputImage::ImageDimension);
- itkStaticConstMacro(OutputImageDimension, unsigned int,
- TInputImage::ImageDimension);
- itkStaticConstMacro(ImageDimension, unsigned int,
- TInputImage::ImageDimension);
-
- typedef typename itk::BinaryImageToLabelMapFilter< InputImageType, OutputImageType > LabelizerType;
- typedef typename itk::ShapeLabelMapFilter< OutputImageType > LabelObjectValuatorType;
-
- /** Standard New method. */
- itkNewMacro(Self);
-
- /** Runtime information support. */
- itkTypeMacro(BinaryImageToShapeLabelMapFilter,
- 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, InputImagePixelType);
- itkGetConstMacro(ForegroundValue, InputImagePixelType);
-
- /**
- * Set/Get whether the maximum Feret diameter should be computed or not. The
- * defaut value is false, because of the high computation time required.
- */
- itkSetMacro(ComputeFeretDiameter, bool);
- itkGetConstReferenceMacro(ComputeFeretDiameter, bool);
- itkBooleanMacro(ComputeFeretDiameter);
-
- /**
- * Set/Get whether the perimeter should be computed or not. The defaut value
- * is false, because of the high computation time required.
- */
- itkSetMacro(ComputePerimeter, bool);
- itkGetConstReferenceMacro(ComputePerimeter, bool);
- itkBooleanMacro(ComputePerimeter);
-
-
-protected:
- BinaryImageToShapeLabelMapFilter();
- ~BinaryImageToShapeLabelMapFilter() {};
- void PrintSelf(std::ostream& os, Indent indent) const;
-
- /** BinaryImageToShapeLabelMapFilter needs the entire input be
- * available. Thus, it needs to provide an implementation of
- * GenerateInputRequestedRegion(). */
- void GenerateInputRequestedRegion() ;
-
- /** BinaryImageToShapeLabelMapFilter will produce the entire output. */
- void EnlargeOutputRequestedRegion(DataObject *itkNotUsed(output));
-
- /** Single-threaded version of GenerateData. This filter delegates
- * to GrayscaleGeodesicErodeImageFilter. */
- void GenerateData();
-
-
-private:
- BinaryImageToShapeLabelMapFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
- bool m_FullyConnected;
- OutputImagePixelType m_BackgroundValue;
- InputImagePixelType m_ForegroundValue;
- bool m_ComputeFeretDiameter;
- bool m_ComputePerimeter;
-
-} ; // end of class
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkBinaryImageToShapeLabelMapFilter.txx"
-#endif
-
-#endif
-
-
diff --git a/Utilities/InsightJournal/itkBinaryImageToShapeLabelMapFilter.txx b/Utilities/InsightJournal/itkBinaryImageToShapeLabelMapFilter.txx
deleted file mode 100644
index 61d3dfbfa71527f3b2893a01c013e0d18a49eaf0..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkBinaryImageToShapeLabelMapFilter.txx
+++ /dev/null
@@ -1,112 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkBinaryImageToShapeLabelMapFilter.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 __itkBinaryImageToShapeLabelMapFilter_txx
-#define __itkBinaryImageToShapeLabelMapFilter_txx
-
-#include "itkBinaryImageToShapeLabelMapFilter.h"
-#include "itkProgressAccumulator.h"
-
-
-namespace itk {
-
-template<class TInputImage, class TOutputImage>
-BinaryImageToShapeLabelMapFilter<TInputImage, TOutputImage>
-::BinaryImageToShapeLabelMapFilter()
-{
- m_BackgroundValue = NumericTraits<OutputImagePixelType>::NonpositiveMin();
- m_ForegroundValue = NumericTraits<OutputImagePixelType>::max();
- m_FullyConnected = false;
- m_ComputeFeretDiameter = false;
- m_ComputePerimeter = false;
-}
-
-template<class TInputImage, class TOutputImage>
-void
-BinaryImageToShapeLabelMapFilter<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 )
- {
- input->SetRequestedRegion( input->GetLargestPossibleRegion() );
- }
-}
-
-
-template<class TInputImage, class TOutputImage>
-void
-BinaryImageToShapeLabelMapFilter<TInputImage, TOutputImage>
-::EnlargeOutputRequestedRegion(DataObject *)
-{
- this->GetOutput()
- ->SetRequestedRegion( this->GetOutput()->GetLargestPossibleRegion() );
-}
-
-
-template<class TInputImage, class TOutputImage>
-void
-BinaryImageToShapeLabelMapFilter<TInputImage, TOutputImage>
-::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, .5f);
-
- typename LabelObjectValuatorType::Pointer valuator = LabelObjectValuatorType::New();
- valuator->SetInput( labelizer->GetOutput() );
- valuator->SetNumberOfThreads( this->GetNumberOfThreads() );
- valuator->SetComputePerimeter( m_ComputePerimeter );
- valuator->SetComputeFeretDiameter( m_ComputeFeretDiameter );
- progress->RegisterInternalFilter(valuator, .5f);
-
- valuator->GraftOutput( this->GetOutput() );
- valuator->Update();
- this->GraftOutput( valuator->GetOutput() );
-}
-
-
-template<class TInputImage, class TOutputImage>
-void
-BinaryImageToShapeLabelMapFilter<TInputImage, TOutputImage>
-::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 << "ComputeFeretDiameter: " << m_ComputeFeretDiameter << std::endl;
- os << indent << "ComputePerimeter: " << m_ComputePerimeter << std::endl;
-}
-
-}// end namespace itk
-#endif
diff --git a/Utilities/InsightJournal/itkBinaryImageToStatisticsLabelMapFilter.h b/Utilities/InsightJournal/itkBinaryImageToStatisticsLabelMapFilter.h
deleted file mode 100644
index 9e339f4bcb64a5a5b00775c0cacbbb1e14b8fcdb..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkBinaryImageToStatisticsLabelMapFilter.h
+++ /dev/null
@@ -1,222 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkBinaryImageToStatisticsLabelMapFilter.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 __itkBinaryImageToStatisticsLabelMapFilter_h
-#define __itkBinaryImageToStatisticsLabelMapFilter_h
-
-#include "itkImageToImageFilter.h"
-#include "itkStatisticsLabelObject.h"
-#include "itkLabelMap.h"
-#include "itkBinaryImageToLabelMapFilter.h"
-#include "itkStatisticsLabelMapFilter.h"
-
-
-namespace itk {
-
-/** \class BinaryImageToStatisticsLabelMapFilter
- * \brief a convenient class to convert a binary image to a label map and valuate the statistics attributes at once
- *
- * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
- *
- * \sa StatisticsLabelObject, LabelStatisticsOpeningImageFilter, BinaryStatisticsOpeningImageFilter
- * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
- */
-template<class TInputImage, class TFeatureImage, class TOutputImage=LabelMap< StatisticsLabelObject< unsigned long, TInputImage::ImageDimension > > >
-class ITK_EXPORT BinaryImageToStatisticsLabelMapFilter :
- public ImageToImageFilter<TInputImage, TOutputImage>
-{
-public:
- /** Standard class typedefs. */
- typedef BinaryImageToStatisticsLabelMapFilter Self;
- typedef ImageToImageFilter<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 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::LabelObjectType LabelObjectType;
-
- 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 typename itk::BinaryImageToLabelMapFilter< InputImageType, OutputImageType > LabelizerType;
- typedef typename itk::StatisticsLabelMapFilter< OutputImageType, FeatureImageType > LabelObjectValuatorType;
-
- /** Standard New method. */
- itkNewMacro(Self);
-
- /** Runtime information support. */
- itkTypeMacro(BinaryImageToStatisticsLabelMapFilter,
- 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, InputImagePixelType);
- itkGetConstMacro(ForegroundValue, InputImagePixelType);
-
- /**
- * Set/Get whether the maximum Feret diameter should be computed or not. The
- * defaut value is false, because of the high computation time required.
- */
- itkSetMacro(ComputeFeretDiameter, bool);
- itkGetConstReferenceMacro(ComputeFeretDiameter, bool);
- itkBooleanMacro(ComputeFeretDiameter);
-
- /**
- * Set/Get whether the perimeter should be computed or not. The defaut value
- * is false, because of the high computation time required.
- */
- itkSetMacro(ComputePerimeter, bool);
- itkGetConstReferenceMacro(ComputePerimeter, bool);
- itkBooleanMacro(ComputePerimeter);
-
- /** 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 );
- }
-
- /**
- * Set/Get whether the histogram should be attached to the label object or not.
- * This option defaults to `true`, but because the histogram may take a lot of memory
- * compared to the other attributes, this option is useful to reduce the memory usage
- * when the histogram is not required.
- */
- itkSetMacro(ComputeHistogram, bool);
- itkGetConstReferenceMacro(ComputeHistogram, bool);
- itkBooleanMacro(ComputeHistogram);
-
- /**
- * Set/Get the number of bins in the histogram. Note that the histogram is used
- * to compute the median value, and that this option may have an effect on the
- * value of the median.
- */
- itkSetMacro(NumberOfBins, unsigned int);
- itkGetConstReferenceMacro(NumberOfBins, unsigned int);
-
-
-
-protected:
- BinaryImageToStatisticsLabelMapFilter();
- ~BinaryImageToStatisticsLabelMapFilter() {};
- void PrintSelf(std::ostream& os, Indent indent) const;
-
- /** BinaryImageToStatisticsLabelMapFilter needs the entire input be
- * available. Thus, it needs to provide an implementation of
- * GenerateInputRequestedRegion(). */
- void GenerateInputRequestedRegion() ;
-
- /** BinaryImageToStatisticsLabelMapFilter will produce the entire output. */
- void EnlargeOutputRequestedRegion(DataObject *itkNotUsed(output));
-
- /** Single-threaded version of GenerateData. This filter delegates
- * to GrayscaleGeodesicErodeImageFilter. */
- void GenerateData();
-
-
-private:
- BinaryImageToStatisticsLabelMapFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
- bool m_FullyConnected;
- OutputImagePixelType m_BackgroundValue;
- InputImagePixelType m_ForegroundValue;
- bool m_ComputeFeretDiameter;
- bool m_ComputePerimeter;
- unsigned int m_NumberOfBins;
- bool m_ComputeHistogram;
-
-} ; // end of class
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkBinaryImageToStatisticsLabelMapFilter.txx"
-#endif
-
-#endif
-
-
diff --git a/Utilities/InsightJournal/itkBinaryImageToStatisticsLabelMapFilter.txx b/Utilities/InsightJournal/itkBinaryImageToStatisticsLabelMapFilter.txx
deleted file mode 100644
index 914fa7c7a879f10c4b9114bef09aa6a15ea53352..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkBinaryImageToStatisticsLabelMapFilter.txx
+++ /dev/null
@@ -1,120 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkBinaryImageToStatisticsLabelMapFilter.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 __itkBinaryImageToStatisticsLabelMapFilter_txx
-#define __itkBinaryImageToStatisticsLabelMapFilter_txx
-
-#include "itkBinaryImageToStatisticsLabelMapFilter.h"
-#include "itkProgressAccumulator.h"
-
-
-namespace itk {
-
-template<class TInputImage, class TFeatureImage, class TOutputImage>
-BinaryImageToStatisticsLabelMapFilter<TInputImage, TFeatureImage, TOutputImage>
-::BinaryImageToStatisticsLabelMapFilter()
-{
- m_BackgroundValue = NumericTraits<OutputImagePixelType>::NonpositiveMin();
- m_ForegroundValue = NumericTraits<OutputImagePixelType>::max();
- m_FullyConnected = false;
- m_ComputeFeretDiameter = false;
- m_ComputePerimeter = false;
- m_NumberOfBins = 128;
- m_ComputeHistogram = true;
- this->SetNumberOfRequiredInputs(2);
-}
-
-template<class TInputImage, class TFeatureImage, class TOutputImage>
-void
-BinaryImageToStatisticsLabelMapFilter<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 )
- {
- input->SetRequestedRegion( input->GetLargestPossibleRegion() );
- }
-}
-
-
-template<class TInputImage, class TFeatureImage, class TOutputImage>
-void
-BinaryImageToStatisticsLabelMapFilter<TInputImage, TFeatureImage, TOutputImage>
-::EnlargeOutputRequestedRegion(DataObject *)
-{
- this->GetOutput()
- ->SetRequestedRegion( this->GetOutput()->GetLargestPossibleRegion() );
-}
-
-
-template<class TInputImage, class TFeatureImage, class TOutputImage>
-void
-BinaryImageToStatisticsLabelMapFilter<TInputImage, TFeatureImage, TOutputImage>
-::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, .5f);
-
- typename LabelObjectValuatorType::Pointer valuator = LabelObjectValuatorType::New();
- valuator->SetInput( labelizer->GetOutput() );
- valuator->SetFeatureImage( this->GetFeatureImage() );
- valuator->SetNumberOfThreads( this->GetNumberOfThreads() );
- valuator->SetComputePerimeter( m_ComputePerimeter );
- valuator->SetComputeFeretDiameter( m_ComputeFeretDiameter );
- valuator->SetComputeHistogram( m_ComputeHistogram );
- valuator->SetNumberOfBins( m_NumberOfBins );
- progress->RegisterInternalFilter(valuator, .5f);
-
- valuator->GraftOutput( this->GetOutput() );
- valuator->Update();
- this->GraftOutput( valuator->GetOutput() );
-}
-
-
-template<class TInputImage, class TFeatureImage, class TOutputImage>
-void
-BinaryImageToStatisticsLabelMapFilter<TInputImage, TFeatureImage, TOutputImage>
-::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 << "ComputeFeretDiameter: " << m_ComputeFeretDiameter << std::endl;
- os << indent << "ComputePerimeter: " << m_ComputePerimeter << std::endl;
- os << indent << "ComputeHistogram: " << m_ComputeHistogram << std::endl;
- os << indent << "NumberOfBins: " << m_NumberOfBins << std::endl;
-}
-
-}// end namespace itk
-#endif
diff --git a/Utilities/InsightJournal/itkChangeRegionLabelMapFilter.h b/Utilities/InsightJournal/itkChangeRegionLabelMapFilter.h
deleted file mode 100644
index d80004758db28cb9977485437490da31f6896c77..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkChangeRegionLabelMapFilter.h
+++ /dev/null
@@ -1,120 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkChangeRegionLabelMapFilter.h,v $
- Language: C++
- Date: $Date: 2004/07/11 14:56:38 $
- 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.
-
- Portions of this code are covered under the VTK copyright.
- See VTKCopyright.txt or http://www.kitware.com/VTKCopyright.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 __itkChangeRegionLabelMapFilter_h
-#define __itkChangeRegionLabelMapFilter_h
-
-#include "itkInPlaceLabelMapFilter.h"
-
-namespace itk
-{
-
-/** \class ChangeRegionLabelMapFilter
- * \brief Change the region of a label map
- *
- * Change the region of a label map. If the output can't contain some lines of
- * the objects, they are truncated, or remove. All the objects fully outside the
- * output region are removed.
- *
- * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
- *
- * \sa LabelMapMaskImageFilter
- * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
- */
-template <class TInputImage>
-class ITK_EXPORT ChangeRegionLabelMapFilter : public InPlaceLabelMapFilter<TInputImage>
-{
-public:
- /** Standard class typedefs. */
- typedef ChangeRegionLabelMapFilter Self;
- typedef InPlaceLabelMapFilter<TInputImage> Superclass;
- typedef SmartPointer<Self> Pointer;
- typedef SmartPointer<const Self> ConstPointer;
-
-
- /** Run-time type information (and related methods). */
- itkTypeMacro(ChangeRegionLabelMapFilter, InPlaceImageFilter);
-
- /** Standard New method. */
- itkNewMacro(Self);
-
- /** Superclass typedefs. */
- typedef typename Superclass::OutputImageType OutputImageType;
- typedef typename Superclass::OutputImagePointer OutputImagePointer;
- typedef typename Superclass::OutputImageRegionType OutputImageRegionType;
- typedef typename Superclass::OutputImagePixelType OutputImagePixelType;
-
- /** 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 InputImageType::PixelType PixelType;
- typedef typename InputImageType::IndexType IndexType;
- typedef typename InputImageType::SizeType SizeType;
- typedef typename InputImageType::RegionType RegionType;
-
- typedef TInputImage TOutputImage;
-
- /** ImageDimension constants */
- itkStaticConstMacro(InputImageDimension, unsigned int,
- TInputImage::ImageDimension);
- itkStaticConstMacro(OutputImageDimension, unsigned int,
- TOutputImage::ImageDimension);
- itkStaticConstMacro(ImageDimension, unsigned int,
- TOutputImage::ImageDimension);
-
- /** The output region to use */
- itkSetMacro(Region, OutputImageRegionType);
- itkGetConstReferenceMacro(Region, OutputImageRegionType);
-
- protected:
- ChangeRegionLabelMapFilter() {};
- ~ChangeRegionLabelMapFilter() {};
-
- virtual void PrintSelf(std::ostream& os, Indent indent) const;
-
- virtual void ThreadedGenerateData( LabelObjectType * labelObject );
-
- void GenerateInputRequestedRegion() ;
-
- void EnlargeOutputRequestedRegion(DataObject *itkNotUsed(output));
-
- virtual void GenerateOutputInformation();
-
- void GenerateData();
-
-private:
- ChangeRegionLabelMapFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
- OutputImageRegionType m_Region;
-
-};
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkChangeRegionLabelMapFilter.txx"
-#endif
-
-#endif
diff --git a/Utilities/InsightJournal/itkChangeRegionLabelMapFilter.txx b/Utilities/InsightJournal/itkChangeRegionLabelMapFilter.txx
deleted file mode 100644
index 2b43e2210c793c07fbbf027bb8f8b59f76aaeaa6..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkChangeRegionLabelMapFilter.txx
+++ /dev/null
@@ -1,167 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkChangeRegionLabelMapFilter.txx,v $
- Language: C++
- Date: $Date: 2004/07/11 14:56:39 $
- 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.
-
- Portions of this code are covered under the VTK copyright.
- See VTKCopyright.txt or http://www.kitware.com/VTKCopyright.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 _itkChangeRegionLabelMapFilter_txx
-#define _itkChangeRegionLabelMapFilter_txx
-#include "itkChangeRegionLabelMapFilter.h"
-
-
-namespace itk
-{
-
-
-template <class TInputImage>
-void
-ChangeRegionLabelMapFilter<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 )
- { return; }
- input->SetRequestedRegion( input->GetLargestPossibleRegion() );
-}
-
-template <class TInputImage>
-void
-ChangeRegionLabelMapFilter<TInputImage>
-::GenerateOutputInformation()
-{
- Superclass::GenerateOutputInformation();
- this->GetOutput()->SetLargestPossibleRegion( m_Region );
-// std::cout << "ChangeRegionLabelMapFilter::GenerateOutputInformation(): " << this->GetOutput()->GetLargestPossibleRegion() << std::endl;
-}
-
-template <class TInputImage>
-void
-ChangeRegionLabelMapFilter<TInputImage>
-::EnlargeOutputRequestedRegion(DataObject *)
-{
- this->GetOutput()
- ->SetRequestedRegion( this->GetOutput()->GetLargestPossibleRegion() );
-}
-
-template <class TInputImage>
-void
-ChangeRegionLabelMapFilter<TInputImage>
-::GenerateData()
-{
-// std::cout << "ChangeRegionLabelMapFilter::GenerateData(): " << this->GetOutput()->GetLargestPossibleRegion() << std::endl;
-
- if( m_Region.IsInside( this->GetInput()->GetLargestPossibleRegion() ) )
- {
- // only copy the image, and do nothing much
- // oh, we have to pretend we have a progress !
- ProgressReporter progress( this, 0, 1 );
- this->AllocateOutputs();
-// std::cout << "do nothing" << std::endl;
- }
- else
- {
- // call the superclass implementation so it will take care to create the threads
- Superclass::GenerateData();
- }
-}
-
-
-template<class TInputImage>
-void
-ChangeRegionLabelMapFilter<TInputImage>
-::ThreadedGenerateData( LabelObjectType * labelObject )
-{
- typename InputImageType::LabelObjectType::LineContainerType::const_iterator lit;
- typename InputImageType::LabelObjectType::LineContainerType lineContainer = labelObject->GetLineContainer();
- labelObject->GetLineContainer().clear();
-// std::cout << "lineContainer.size(): " << lineContainer.size() << std::endl;
-
- IndexType idxMin = m_Region.GetIndex();
- IndexType idxMax;
- for( int i=0; i<ImageDimension; i++ )
- {
- idxMax[i] = idxMin[i] + m_Region.GetSize()[i] - 1;
- }
-// std::cout << "idxMin: " << idxMin << std::endl;
-// std::cout << "idxMax: " << idxMax << std::endl;
-
- for( lit = lineContainer.begin(); lit != lineContainer.end(); lit++ )
- {
- IndexType idx = lit->GetIndex();
- unsigned long length = lit->GetLength();
-
- bool outside = false;
- for( int i=1; i<ImageDimension; i++ )
- {
- if( idx[i] < idxMin[i] || idx[i] > idxMax[i] )
- {
- outside = true;
- }
- }
- // check the axis 0
- if( !outside )
- {
- long lastIdx0 = idx[0] + length - 1;
- if( !( ( idx[0] < idxMin[0] && lastIdx0 < idxMin[0] )
- || ( idx[0] > idxMax[0] && lastIdx0 > idxMax[0] ) ) )
- {
-// std::cout << "!outside" << std::endl;
- IndexType newIdx = idx;
- long newLength = length;
- if( idx[0] < idxMin[0] )
- {
- newLength -= idxMin[0] - idx[0];
- newIdx[0] = idxMin[0];
- }
- if( lastIdx0 > idxMax[0] )
- {
- newLength -= lastIdx0 - idxMax[0];
- }
-
- labelObject->AddLine( newIdx, newLength );
- }
- }
-
- }
-
- // remove the object if it is empty
- if( labelObject->GetLineContainer().empty() )
- {
-// std::cout << "remove: " << labelObject << std::endl;
- this->m_LabelObjectContainerLock->Lock();
- this->GetOutput()->RemoveLabelObject( labelObject );
- this->m_LabelObjectContainerLock->Unlock();
- }
-
-}
-
-template<class TInputImage>
-void
-ChangeRegionLabelMapFilter<TInputImage>
-::PrintSelf(std::ostream& os, Indent indent) const
-{
- Superclass::PrintSelf(os, indent);
- os << indent << "Region: " << m_Region << std::endl;
-}
-
-
-} // end namespace itk
-
-#endif
diff --git a/Utilities/InsightJournal/itkCropLabelMapFilter.h b/Utilities/InsightJournal/itkCropLabelMapFilter.h
deleted file mode 100644
index 7bced2c1274f05d3a7468a8ef0fad8dc8199d266..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkCropLabelMapFilter.h
+++ /dev/null
@@ -1,130 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkCropLabelMapFilter.h,v $
- Language: C++
- Date: $Date: 2004/07/11 14:56:38 $
- 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.
-
- Portions of this code are covered under the VTK copyright.
- See VTKCopyright.txt or http://www.kitware.com/VTKCopyright.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 __itkCropLabelMapFilter_h
-#define __itkCropLabelMapFilter_h
-
-#include "itkChangeRegionLabelMapFilter.h"
-
-namespace itk
-{
-
-/** \class CropLabelMapFilter
- * \brief Crop a LabelMap image
- *
- * Crop a label map. If the output can't contain some lines of
- * the objects, they are truncated, or remove. All the objects fully outside the
- * output region are removed.
- *
- * The SetCropSize() method can be used to set the crop size of the lower and
- * the upper boundaries in a single call.
- * By default, the filter doesn't crop anything.
- *
- * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
- *
- * \sa PadLabelMapFilter
- * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
- */
-template <class TInputImage>
-class ITK_EXPORT CropLabelMapFilter : public ChangeRegionLabelMapFilter<TInputImage>
-{
-public:
- /** Standard class typedefs. */
- typedef CropLabelMapFilter Self;
- typedef ChangeRegionLabelMapFilter<TInputImage> Superclass;
- typedef SmartPointer<Self> Pointer;
- typedef SmartPointer<const Self> ConstPointer;
-
-
- /** Run-time type information (and related methods). */
- itkTypeMacro(CropLabelMapFilter, ChangeRegionImageFilter);
-
- /** Standard New method. */
- itkNewMacro(Self);
-
- /** Superclass typedefs. */
- typedef typename Superclass::OutputImageType OutputImageType;
- typedef typename Superclass::OutputImagePointer OutputImagePointer;
- typedef typename Superclass::OutputImageRegionType OutputImageRegionType;
- typedef typename Superclass::OutputImagePixelType OutputImagePixelType;
-
- /** 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 InputImageType::PixelType PixelType;
- typedef typename InputImageType::IndexType IndexType;
- typedef typename InputImageType::SizeType SizeType;
- typedef typename InputImageType::RegionType RegionType;
-
- typedef TInputImage TOutputImage;
-
- /** ImageDimension constants */
- itkStaticConstMacro(InputImageDimension, unsigned int,
- TInputImage::ImageDimension);
- itkStaticConstMacro(OutputImageDimension, unsigned int,
- TOutputImage::ImageDimension);
- itkStaticConstMacro(ImageDimension, unsigned int,
- TOutputImage::ImageDimension);
-
- /** Set/Get the cropping sizes for the upper and lower boundaries. */
- itkSetMacro(UpperBoundaryCropSize, SizeType);
- itkGetMacro(UpperBoundaryCropSize, SizeType);
- itkSetMacro(LowerBoundaryCropSize, SizeType);
- itkGetMacro(LowerBoundaryCropSize, SizeType);
-
- void SetCropSize( const SizeType & size )
- {
- this->SetUpperBoundaryCropSize( size );
- this->SetLowerBoundaryCropSize( size );
- }
-
-
- protected:
- CropLabelMapFilter()
- {
- m_UpperBoundaryCropSize.Fill(0);
- m_LowerBoundaryCropSize.Fill(0);
- };
- ~CropLabelMapFilter() {};
-
- virtual void GenerateOutputInformation();
-
- void PrintSelf(std::ostream& os, Indent indent) const;
-
-
-private:
- CropLabelMapFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
- SizeType m_UpperBoundaryCropSize;
- SizeType m_LowerBoundaryCropSize;
-};
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkCropLabelMapFilter.txx"
-#endif
-
-#endif
diff --git a/Utilities/InsightJournal/itkCropLabelMapFilter.txx b/Utilities/InsightJournal/itkCropLabelMapFilter.txx
deleted file mode 100644
index 55392c65a2217b045729c67d3629a7b75224adae..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkCropLabelMapFilter.txx
+++ /dev/null
@@ -1,79 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkCropLabelMapFilter.txx,v $
- Language: C++
- Date: $Date: 2004/07/11 14:56:39 $
- 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.
-
- Portions of this code are covered under the VTK copyright.
- See VTKCopyright.txt or http://www.kitware.com/VTKCopyright.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 _itkCropLabelMapFilter_txx
-#define _itkCropLabelMapFilter_txx
-#include "itkCropLabelMapFilter.h"
-
-
-namespace itk
-{
-
-
-template <class TInputImage>
-void
-CropLabelMapFilter<TInputImage>
-::GenerateOutputInformation()
-{
- const TInputImage * inputPtr = this->GetInput();
- if( !inputPtr )
- {
- return;
- }
-
- // Compute the new region size.
- RegionType croppedRegion;
- SizeType sz;
- IndexType idx;
-
- SizeType input_sz =
- inputPtr->GetLargestPossibleRegion().GetSize();
- IndexType input_idx =
- inputPtr->GetLargestPossibleRegion().GetIndex();
-
- idx = input_idx + m_LowerBoundaryCropSize;
- sz = input_sz - (m_UpperBoundaryCropSize + m_LowerBoundaryCropSize);
-
- croppedRegion.SetSize(sz);
- croppedRegion.SetIndex(idx);
-
- // Set extraction region in the superclass.
- this->SetRegion(croppedRegion);
-
- //
- Superclass::GenerateOutputInformation();
-}
-
-
-template <class TInputImage>
-void
-CropLabelMapFilter<TInputImage>
-::PrintSelf(std::ostream& os, Indent indent) const
-{
- Superclass::PrintSelf(os,indent);
-
- os << indent << "UpperBoundaryCropSize: " << m_UpperBoundaryCropSize <<
- std::endl;
- os << indent << "LowerBoundaryCropSize: " << m_LowerBoundaryCropSize <<
- std::endl;
-}
-
-} // end namespace itk
-
-#endif
diff --git a/Utilities/InsightJournal/itkInPlaceLabelMapFilter.h b/Utilities/InsightJournal/itkInPlaceLabelMapFilter.h
deleted file mode 100644
index 39c22e241e1bec0f9159cf71f219c21fe3a2665d..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkInPlaceLabelMapFilter.h
+++ /dev/null
@@ -1,179 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkInPlaceLabelMapFilter.h,v $
- Language: C++
- Date: $Date: 2004/07/11 14:56:38 $
- 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.
-
- Portions of this code are covered under the VTK copyright.
- See VTKCopyright.txt or http://www.kitware.com/VTKCopyright.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 __itkInPlaceLabelMapFilter_h
-#define __itkInPlaceLabelMapFilter_h
-
-#include "itkLabelMapFilter.h"
-
-namespace itk
-{
-
-/** \class InPlaceLabelMapFilter
- * \brief Base class for filters that take an image as input and overwrite that image as the output
- *
- * InPlaceLabelMapFilter is the base class for all process objects whose
- * output image data is constructed by overwriting the input image
- * data. In other words, the output bulk data is the same block of
- * memory as the input bulk data. This filter provides the mechanisms
- * for in place image processing while maintaining general pipeline
- * mechanics. InPlaceLabelMapFilters use less memory than standard
- * ImageToImageFilters because the input buffer is reused as the
- * output buffer. However, this benefit does not come without a cost.
- * Since the filter overwrites its input, the ownership of the bulk
- * data is transitioned from the input data object to the output data
- * object. When a data object has multiple consumers with one
- * of the consumers being an in place filter, the in place filter
- * effectively destroys the bulk data for the data object. Upstream
- * filters will then have to re-execute to regenerate the data object's
- * bulk data for the remaining consumers.
- *
- * Since an InPlaceLabelMapFilter reuses the input bulk data memory for the
- * output bulk data memory, the input image type must match the output
- * image type. If the input and output image types are not identical,
- * the filter reverts to a traditional ImageToImageFilter behaviour
- * where an output image is allocated. In place operation can also be
- * controlled (when the input and output image type match) via the
- * methods InPlaceOn() and InPlaceOff().
- *
- * Subclasses of InPlaceLabelMapFilter must take extra care in how they
- * manage memory using (and perhaps overriding) the implementations of
- * ReleaseInputs() and AllocateOutputs() provided here.
- *
- * \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 ITK_EXPORT InPlaceLabelMapFilter : public LabelMapFilter<TInputImage, TInputImage>
-{
-public:
- /** Standard class typedefs. */
- typedef InPlaceLabelMapFilter Self;
- typedef LabelMapFilter<TInputImage, TInputImage> Superclass;
- typedef SmartPointer<Self> Pointer;
- typedef SmartPointer<const Self> ConstPointer;
-
-
- /** Run-time type information (and related methods). */
- itkTypeMacro(InPlaceLabelMapFilter, LabelMapFilter);
-
- /** Standard New method. */
- itkNewMacro(Self);
-
- /** Superclass typedefs. */
- typedef typename Superclass::OutputImageType OutputImageType;
- typedef typename Superclass::OutputImagePointer OutputImagePointer;
- typedef typename Superclass::OutputImageRegionType OutputImageRegionType;
- typedef typename Superclass::OutputImagePixelType OutputImagePixelType;
-
- /** 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 InputImageType::PixelType PixelType;
- typedef typename InputImageType::IndexType IndexType;
- typedef typename InputImageType::RegionType RegionType;
-
- typedef TInputImage TOutputImage;
-
- /** ImageDimension constants */
- itkStaticConstMacro(InputImageDimension, unsigned int,
- TInputImage::ImageDimension);
- itkStaticConstMacro(OutputImageDimension, unsigned int,
- TOutputImage::ImageDimension);
-
- /** In place operation can be turned on and off. This only has an
- * effect when the input and output image type match. */
- itkSetMacro(InPlace, bool);
- itkGetMacro(InPlace, bool);
- itkBooleanMacro(InPlace);
-
- /** Can the filter run in place? To do so, the filter's first input
- * and output must have the same dimension and pixel type. This
- * method can be used in conjunction with the InPlace ivar to
- * determine whether a particular use of the filter is really
- * running in place. Some filters may be able to optimize their
- * operation if the InPlace is true and CanRunInPlace is true. */
- bool CanRunInPlace() const
- {
- return (typeid(TInputImage) == typeid(TOutputImage));
- };
-
- protected:
- InPlaceLabelMapFilter();
- ~InPlaceLabelMapFilter();
-
- virtual void PrintSelf(std::ostream& os, Indent indent) const;
-
- /** The GenerateData method normally allocates the buffers for all
- * of the outputs of a filter. Since InPlaceLabelMapFilter's can use an
- * overwritten version of the input for its output, the output
- * buffer should not be allocated. When possible, we graft the input
- * to the filter to the output. If an InPlaceFilter has multiple
- * outputs, then it would need to override this method to graft one
- * of its outputs and allocate the remaining. If a filter is
- * threaded (i.e. it provides an implementation of
- * ThreadedGenerateData()), this method is called automatically. If
- * an InPlaceFilter is not threaded (i.e. it provides an
- * implementation of GenerateData()), then this method (or
- * equivalent) must be called in GenerateData(). */
- virtual void AllocateOutputs();
-
- /** InPlaceLabelMapFilter may transfer ownership of the input bulk data
- * to the output object. Once the output object owns the bulk data
- * (done in AllocateOutputs()), the input object must release its
- * hold on the bulk data. ProcessObject::ReleaseInputs() only
- * releases the input bulk data when the user has set the
- * ReleaseDataFlag. InPlaceLabelMapFilter::ReleaseInputs() also
- * releases the input that it has overwritten.
- *
- * \sa ProcessObject::ReleaseInputs() */
- virtual void ReleaseInputs();
-
-
- /**
- * Return the output label collection image, instead of the input as in the default
- * implementation
- */
- virtual InputImageType * GetLabelMap()
- {
- return this->GetOutput();
- }
-
-private:
- InPlaceLabelMapFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
- bool m_InPlace;
-
-};
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkInPlaceLabelMapFilter.txx"
-#endif
-
-#endif
diff --git a/Utilities/InsightJournal/itkInPlaceLabelMapFilter.txx b/Utilities/InsightJournal/itkInPlaceLabelMapFilter.txx
deleted file mode 100644
index 96c6315a5f79147ebc635d9338970383a1648a31..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkInPlaceLabelMapFilter.txx
+++ /dev/null
@@ -1,146 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkInPlaceLabelMapFilter.txx,v $
- Language: C++
- Date: $Date: 2004/07/11 14:56:39 $
- 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.
-
- Portions of this code are covered under the VTK copyright.
- See VTKCopyright.txt or http://www.kitware.com/VTKCopyright.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 _itkInPlaceLabelMapFilter_txx
-#define _itkInPlaceLabelMapFilter_txx
-#include "itkInPlaceLabelMapFilter.h"
-
-
-namespace itk
-{
-
-/**
- *
- */
-template <class TInputImage>
-InPlaceLabelMapFilter<TInputImage>
-::InPlaceLabelMapFilter()
- : m_InPlace(true)
-{
-}
-
-/**
- *
- */
-template <class TInputImage>
-InPlaceLabelMapFilter<TInputImage>
-::~InPlaceLabelMapFilter()
-{
-}
-
-
-
-template<class TInputImage>
-void
-InPlaceLabelMapFilter<TInputImage>
-::PrintSelf(std::ostream& os, Indent indent) const
-{
- Superclass::PrintSelf(os, indent);
- os << indent << "InPlace: " << (m_InPlace ? "On" : "Off") << std::endl;
- if ( this->CanRunInPlace())
- {
- os << indent << "The input and output to this filter are the same type. The filter can be run in place." << std::endl;
- }
- else
- {
- os << indent << "The input and output to this filter are different types. The filter cannot be run in place." << std::endl;
- }
-}
-
-template<class TInputImage>
-void
-InPlaceLabelMapFilter<TInputImage>
-::AllocateOutputs()
-{
- // if told to run in place and the types support it,
- if( m_InPlace && this->CanRunInPlace() )
- {
- // Graft this first input to the output. Later, we'll need to
- // remove the input's hold on the bulk data.
- //
- OutputImagePointer inputAsOutput
- = dynamic_cast<TOutputImage *>(const_cast<TInputImage *>(this->GetInput()));
- if (inputAsOutput)
- {
- // save the largest possible region to restore it after the graft output.
- // the largest possible region is not that important with LabelMap and
- // can be managed by the filter, even when running inplace
- RegionType region = this->GetOutput()->GetLargestPossibleRegion();
- this->GraftOutput( inputAsOutput );
- this->GetOutput()->SetRegions( region );
- }
- }
- else
- {
- Superclass::AllocateOutputs();
- // copy the content of the input image to the output image
- const TInputImage * input = this->GetInput();
- TOutputImage * output = this->GetOutput();
- assert( input != NULL );
- assert( output != NULL );
-
- output->SetBackgroundValue( input->GetBackgroundValue() );
-
- typedef typename InputImageType::LabelObjectType LabelObjectType;
-
- typename InputImageType::LabelObjectContainerType::const_iterator it;
- const typename InputImageType::LabelObjectContainerType & labelObjectContainer = input->GetLabelObjectContainer();
- for( it = labelObjectContainer.begin(); it != labelObjectContainer.end(); it++ )
- {
- const LabelObjectType * labeObject = it->second;
- assert( labeObject != NULL );
- assert( labeObject->GetLabel() == it->first );
-
- typename LabelObjectType::Pointer newLabelObject = LabelObjectType::New();
- newLabelObject->CopyAllFrom( labeObject );
-
- output->AddLabelObject( newLabelObject );
- }
-
- }
-}
-
-template<class TInputImage>
-void
-InPlaceLabelMapFilter<TInputImage>
-::ReleaseInputs()
-{
- // if told to run in place and the types support it,
- if (m_InPlace && (typeid(TInputImage) == typeid(TOutputImage)))
- {
- // Release any input where the ReleaseData flag has been set
- ProcessObject::ReleaseInputs();
-
- // Release input 0 by default since we overwrote it
- TInputImage * ptr = const_cast<TInputImage*>( this->GetInput() );
- if( ptr )
- {
- ptr->ReleaseData();
- }
- }
- else
- {
- Superclass::ReleaseInputs();
- }
-}
-
-
-} // end namespace itk
-
-#endif
diff --git a/Utilities/InsightJournal/itkLabelImageToShapeLabelMapFilter.h b/Utilities/InsightJournal/itkLabelImageToShapeLabelMapFilter.h
deleted file mode 100644
index 6c9e9639d13bc8c58f7d804827e7230c0719e84e..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkLabelImageToShapeLabelMapFilter.h
+++ /dev/null
@@ -1,151 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkLabelImageToShapeLabelMapFilter.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 __itkLabelImageToShapeLabelMapFilter_h
-#define __itkLabelImageToShapeLabelMapFilter_h
-
-#include "itkImageToImageFilter.h"
-#include "itkShapeLabelObject.h"
-#include "itkLabelMap.h"
-#include "itkLabelImageToLabelMapFilter.h"
-#include "itkShapeLabelMapFilter.h"
-
-
-namespace itk {
-
-/** \class LabelImageToShapeLabelMapFilter
- * \brief a convenient class to convert a label image to a label map and valuate the shape attributes at once
- *
- * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
- *
- * \sa ShapeLabelObject, LabelShapeOpeningImageFilter, LabelStatisticsOpeningImageFilter
- * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
- */
-template<class TInputImage, class TOutputImage=LabelMap< ShapeLabelObject< typename TInputImage::PixelType, TInputImage::ImageDimension > > >
-class ITK_EXPORT LabelImageToShapeLabelMapFilter :
- public ImageToImageFilter<TInputImage, TOutputImage>
-{
-public:
- /** Standard class typedefs. */
- typedef LabelImageToShapeLabelMapFilter Self;
- typedef ImageToImageFilter<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 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::LabelObjectType LabelObjectType;
-
- /** ImageDimension constants */
- itkStaticConstMacro(InputImageDimension, unsigned int,
- TInputImage::ImageDimension);
- itkStaticConstMacro(OutputImageDimension, unsigned int,
- TInputImage::ImageDimension);
- itkStaticConstMacro(ImageDimension, unsigned int,
- TInputImage::ImageDimension);
-
- typedef typename itk::LabelImageToLabelMapFilter< InputImageType, OutputImageType > LabelizerType;
- typedef typename itk::ShapeLabelMapFilter< OutputImageType > LabelObjectValuatorType;
-
- /** Standard New method. */
- itkNewMacro(Self);
-
- /** Runtime information support. */
- itkTypeMacro(LabelImageToShapeLabelMapFilter,
- 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 whether the maximum Feret diameter should be computed or not. The
- * defaut value is false, because of the high computation time required.
- */
- itkSetMacro(ComputeFeretDiameter, bool);
- itkGetConstReferenceMacro(ComputeFeretDiameter, bool);
- itkBooleanMacro(ComputeFeretDiameter);
-
- /**
- * Set/Get whether the perimeter should be computed or not. The defaut value
- * is false, because of the high computation time required.
- */
- itkSetMacro(ComputePerimeter, bool);
- itkGetConstReferenceMacro(ComputePerimeter, bool);
- itkBooleanMacro(ComputePerimeter);
-
-protected:
- LabelImageToShapeLabelMapFilter();
- ~LabelImageToShapeLabelMapFilter() {};
- void PrintSelf(std::ostream& os, Indent indent) const;
-
- /** LabelImageToShapeLabelMapFilter needs the entire input be
- * available. Thus, it needs to provide an implementation of
- * GenerateInputRequestedRegion(). */
- void GenerateInputRequestedRegion() ;
-
- /** LabelImageToShapeLabelMapFilter will produce the entire output. */
- void EnlargeOutputRequestedRegion(DataObject *itkNotUsed(output));
-
- /** Single-threaded version of GenerateData. This filter delegates
- * to GrayscaleGeodesicErodeImageFilter. */
- void GenerateData();
-
-
-private:
- LabelImageToShapeLabelMapFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
- OutputImagePixelType m_BackgroundValue;
- bool m_ComputeFeretDiameter;
- bool m_ComputePerimeter;
-
-} ; // end of class
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkLabelImageToShapeLabelMapFilter.txx"
-#endif
-
-#endif
-
-
diff --git a/Utilities/InsightJournal/itkLabelImageToShapeLabelMapFilter.txx b/Utilities/InsightJournal/itkLabelImageToShapeLabelMapFilter.txx
deleted file mode 100644
index 53538a575cd74233be4fceea863cbc6b29381cfb..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkLabelImageToShapeLabelMapFilter.txx
+++ /dev/null
@@ -1,106 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkLabelImageToShapeLabelMapFilter.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 __itkLabelImageToShapeLabelMapFilter_txx
-#define __itkLabelImageToShapeLabelMapFilter_txx
-
-#include "itkLabelImageToShapeLabelMapFilter.h"
-#include "itkProgressAccumulator.h"
-
-
-namespace itk {
-
-template<class TInputImage, class TOutputImage>
-LabelImageToShapeLabelMapFilter<TInputImage, TOutputImage>
-::LabelImageToShapeLabelMapFilter()
-{
- m_BackgroundValue = NumericTraits<OutputImagePixelType>::NonpositiveMin();
- m_ComputeFeretDiameter = false;
- m_ComputePerimeter = false;
-}
-
-template<class TInputImage, class TOutputImage>
-void
-LabelImageToShapeLabelMapFilter<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 )
- {
- input->SetRequestedRegion( input->GetLargestPossibleRegion() );
- }
-}
-
-
-template<class TInputImage, class TOutputImage>
-void
-LabelImageToShapeLabelMapFilter<TInputImage, TOutputImage>
-::EnlargeOutputRequestedRegion(DataObject *)
-{
- this->GetOutput()
- ->SetRequestedRegion( this->GetOutput()->GetLargestPossibleRegion() );
-}
-
-
-template<class TInputImage, class TOutputImage>
-void
-LabelImageToShapeLabelMapFilter<TInputImage, TOutputImage>
-::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, .5f);
-
- typename LabelObjectValuatorType::Pointer valuator = LabelObjectValuatorType::New();
- valuator->SetInput( labelizer->GetOutput() );
- valuator->SetNumberOfThreads( this->GetNumberOfThreads() );
- valuator->SetComputePerimeter( m_ComputePerimeter );
- valuator->SetComputeFeretDiameter( m_ComputeFeretDiameter );
- progress->RegisterInternalFilter(valuator, .5f);
-
- valuator->GraftOutput( this->GetOutput() );
- valuator->Update();
- this->GraftOutput( valuator->GetOutput() );
-}
-
-
-template<class TInputImage, class TOutputImage>
-void
-LabelImageToShapeLabelMapFilter<TInputImage, TOutputImage>
-::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 << "ComputeFeretDiameter: " << m_ComputeFeretDiameter << std::endl;
- os << indent << "ComputePerimeter: " << m_ComputePerimeter << std::endl;
-}
-
-}// end namespace itk
-#endif
diff --git a/Utilities/InsightJournal/itkLabelImageToStatisticsLabelMapFilter.h b/Utilities/InsightJournal/itkLabelImageToStatisticsLabelMapFilter.h
deleted file mode 100644
index 4d2caaf525922b760ec74a2803a5a72e2a8b994b..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkLabelImageToStatisticsLabelMapFilter.h
+++ /dev/null
@@ -1,202 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkLabelImageToStatisticsLabelMapFilter.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 __itkLabelImageToStatisticsLabelMapFilter_h
-#define __itkLabelImageToStatisticsLabelMapFilter_h
-
-#include "itkImageToImageFilter.h"
-#include "itkStatisticsLabelObject.h"
-#include "itkLabelMap.h"
-#include "itkLabelImageToLabelMapFilter.h"
-#include "itkStatisticsLabelMapFilter.h"
-
-
-namespace itk {
-
-/** \class LabelImageToStatisticsLabelMapFilter
- * \brief a convenient class to convert a label image to a label map and valuate the statistics attributes at once
- *
- * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
- *
- * \sa StatisticsLabelObject, LabelStatisticsOpeningImageFilter, LabelStatisticsOpeningImageFilter
- * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
- */
-template<class TInputImage, class TFeatureImage, class TOutputImage=LabelMap< StatisticsLabelObject< typename TInputImage::PixelType, TInputImage::ImageDimension > > >
-class ITK_EXPORT LabelImageToStatisticsLabelMapFilter :
- public ImageToImageFilter<TInputImage, TOutputImage>
-{
-public:
- /** Standard class typedefs. */
- typedef LabelImageToStatisticsLabelMapFilter Self;
- typedef ImageToImageFilter<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 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::LabelObjectType LabelObjectType;
-
- 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 typename itk::LabelImageToLabelMapFilter< InputImageType, OutputImageType > LabelizerType;
- typedef typename itk::StatisticsLabelMapFilter< OutputImageType, FeatureImageType > LabelObjectValuatorType;
-
- /** Standard New method. */
- itkNewMacro(Self);
-
- /** Runtime information support. */
- itkTypeMacro(LabelImageToStatisticsLabelMapFilter,
- 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 whether the maximum Feret diameter should be computed or not. The
- * defaut value is false, because of the high computation time required.
- */
- itkSetMacro(ComputeFeretDiameter, bool);
- itkGetConstReferenceMacro(ComputeFeretDiameter, bool);
- itkBooleanMacro(ComputeFeretDiameter);
-
- /**
- * Set/Get whether the perimeter should be computed or not. The defaut value
- * is false, because of the high computation time required.
- */
- itkSetMacro(ComputePerimeter, bool);
- itkGetConstReferenceMacro(ComputePerimeter, bool);
- itkBooleanMacro(ComputePerimeter);
-
- /** 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 );
- }
-
- /**
- * Set/Get whether the histogram should be attached to the label object or not.
- * This option defaults to `true`, but because the histogram may take a lot of memory
- * compared to the other attributes, this option is useful to reduce the memory usage
- * when the histogram is not required.
- */
- itkSetMacro(ComputeHistogram, bool);
- itkGetConstReferenceMacro(ComputeHistogram, bool);
- itkBooleanMacro(ComputeHistogram);
-
- /**
- * Set/Get the number of bins in the histogram. Note that the histogram is used
- * to compute the median value, and that this option may have an effect on the
- * value of the median.
- */
- itkSetMacro(NumberOfBins, unsigned int);
- itkGetConstReferenceMacro(NumberOfBins, unsigned int);
-
-
-protected:
- LabelImageToStatisticsLabelMapFilter();
- ~LabelImageToStatisticsLabelMapFilter() {};
- void PrintSelf(std::ostream& os, Indent indent) const;
-
- /** LabelImageToStatisticsLabelMapFilter needs the entire input be
- * available. Thus, it needs to provide an implementation of
- * GenerateInputRequestedRegion(). */
- void GenerateInputRequestedRegion() ;
-
- /** LabelImageToStatisticsLabelMapFilter will produce the entire output. */
- void EnlargeOutputRequestedRegion(DataObject *itkNotUsed(output));
-
- /** Single-threaded version of GenerateData. This filter delegates
- * to GrayscaleGeodesicErodeImageFilter. */
- void GenerateData();
-
-
-private:
- LabelImageToStatisticsLabelMapFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
- OutputImagePixelType m_BackgroundValue;
- bool m_ComputeFeretDiameter;
- bool m_ComputePerimeter;
- unsigned int m_NumberOfBins;
- bool m_ComputeHistogram;
-
-} ; // end of class
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkLabelImageToStatisticsLabelMapFilter.txx"
-#endif
-
-#endif
-
-
diff --git a/Utilities/InsightJournal/itkLabelImageToStatisticsLabelMapFilter.txx b/Utilities/InsightJournal/itkLabelImageToStatisticsLabelMapFilter.txx
deleted file mode 100644
index e3d707809c5e607ab63fb05221765004cdf44c77..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkLabelImageToStatisticsLabelMapFilter.txx
+++ /dev/null
@@ -1,114 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkLabelImageToStatisticsLabelMapFilter.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 __itkLabelImageToStatisticsLabelMapFilter_txx
-#define __itkLabelImageToStatisticsLabelMapFilter_txx
-
-#include "itkLabelImageToStatisticsLabelMapFilter.h"
-#include "itkProgressAccumulator.h"
-
-
-namespace itk {
-
-template<class TInputImage, class TFeatureImage, class TOutputImage>
-LabelImageToStatisticsLabelMapFilter<TInputImage, TFeatureImage, TOutputImage>
-::LabelImageToStatisticsLabelMapFilter()
-{
- m_BackgroundValue = NumericTraits<OutputImagePixelType>::NonpositiveMin();
- m_ComputeFeretDiameter = false;
- m_ComputePerimeter = false;
- m_NumberOfBins = 128;
- m_ComputeHistogram = true;
- this->SetNumberOfRequiredInputs(2);
-}
-
-template<class TInputImage, class TFeatureImage, class TOutputImage>
-void
-LabelImageToStatisticsLabelMapFilter<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 )
- {
- input->SetRequestedRegion( input->GetLargestPossibleRegion() );
- }
-}
-
-
-template<class TInputImage, class TFeatureImage, class TOutputImage>
-void
-LabelImageToStatisticsLabelMapFilter<TInputImage, TFeatureImage, TOutputImage>
-::EnlargeOutputRequestedRegion(DataObject *)
-{
- this->GetOutput()
- ->SetRequestedRegion( this->GetOutput()->GetLargestPossibleRegion() );
-}
-
-
-template<class TInputImage, class TFeatureImage, class TOutputImage>
-void
-LabelImageToStatisticsLabelMapFilter<TInputImage, TFeatureImage, TOutputImage>
-::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, .5f);
-
- typename LabelObjectValuatorType::Pointer valuator = LabelObjectValuatorType::New();
- valuator->SetInput( labelizer->GetOutput() );
- valuator->SetFeatureImage( this->GetFeatureImage() );
- valuator->SetNumberOfThreads( this->GetNumberOfThreads() );
- valuator->SetComputePerimeter( m_ComputePerimeter );
- valuator->SetComputeFeretDiameter( m_ComputeFeretDiameter );
- valuator->SetComputeHistogram( m_ComputeHistogram );
- valuator->SetNumberOfBins( m_NumberOfBins );
- progress->RegisterInternalFilter(valuator, .5f);
-
- valuator->GraftOutput( this->GetOutput() );
- valuator->Update();
- this->GraftOutput( valuator->GetOutput() );
-}
-
-
-template<class TInputImage, class TFeatureImage, class TOutputImage>
-void
-LabelImageToStatisticsLabelMapFilter<TInputImage, TFeatureImage, TOutputImage>
-::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 << "ComputeFeretDiameter: " << m_ComputeFeretDiameter << std::endl;
- os << indent << "ComputePerimeter: " << m_ComputePerimeter << std::endl;
- os << indent << "ComputeHistogram: " << m_ComputeHistogram << std::endl;
- os << indent << "NumberOfBins: " << m_NumberOfBins << std::endl;
-}
-
-}// end namespace itk
-#endif
diff --git a/Utilities/InsightJournal/itkLabelMapToBinaryImageFilter.h b/Utilities/InsightJournal/itkLabelMapToBinaryImageFilter.h
deleted file mode 100644
index 099fc7ef222f6a2dd650294eaa080d0745ce276d..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkLabelMapToBinaryImageFilter.h
+++ /dev/null
@@ -1,154 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkLabelMapToBinaryImageFilter.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 __itkLabelMapToBinaryImageFilter_h
-#define __itkLabelMapToBinaryImageFilter_h
-
-#include "itkLabelMapFilter.h"
-#include "itkBarrier.h"
-
-namespace itk {
-
-/** \class LabelMapToBinaryImageFilter
- * \brief Convert a LabelMap to a binary image
- *
- * LabelMapToBinaryImageFilter to a binary image. All the objects in the image
- * are used as foreground.
- * The background values of the original binary image can be restored by passing this image
- * to the filter with the SetBackgroundImage() method.
- *
- * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
- *
- * \sa LabelMapToLabelImageFilter, LabelMapMaskImageFilter
- * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
- */
-template<class TInputImage, class TOutputImage>
-class ITK_EXPORT LabelMapToBinaryImageFilter :
- public LabelMapFilter<TInputImage, TOutputImage>
-{
-public:
- /** Standard class typedefs. */
- typedef LabelMapToBinaryImageFilter 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;
-
- /** ImageDimension constants */
- itkStaticConstMacro(InputImageDimension, unsigned int,
- TInputImage::ImageDimension);
- itkStaticConstMacro(OutputImageDimension, unsigned int,
- TOutputImage::ImageDimension);
-
- /** Standard New method. */
- itkNewMacro(Self);
-
- /** Runtime information support. */
- itkTypeMacro(LabelMapToBinaryImageFilter,
- ImageToImageFilter);
-
- /**
- * 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 background image top be used to restore the background values */
- void SetBackgroundImage( const OutputImageType *input)
- {
- // Process object is not const-correct so the const casting is required.
- this->SetNthInput( 1, const_cast<OutputImageType *>(input) );
- }
-
- OutputImageType * GetBackgroundImage()
- {
- return static_cast<OutputImageType*>(const_cast<DataObject *>(this->ProcessObject::GetInput(1)));
- }
-
- /** Set the input image */
- void SetInput1( const InputImageType * input )
- {
- this->SetInput( input );
- }
-
- /** Set the marker image */
- void SetInput2( const OutputImageType * input )
- {
- this->SetBackgroundImage( input );
- }
-
-protected:
- LabelMapToBinaryImageFilter();
- ~LabelMapToBinaryImageFilter() {};
-
- /** LabelMapToBinaryImageFilter needs the entire input be
- * available. Thus, it needs to provide an implementation of
- * GenerateInputRequestedRegion(). */
- void GenerateInputRequestedRegion() ;
-
- /** LabelMapToBinaryImageFilter 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 );
-
-
-private:
- LabelMapToBinaryImageFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
- OutputImagePixelType m_BackgroundValue;
- OutputImagePixelType m_ForegroundValue;
-
- typename Barrier::Pointer m_Barrier;
-
-} ; // end of class
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkLabelMapToBinaryImageFilter.txx"
-#endif
-
-#endif
-
-
diff --git a/Utilities/InsightJournal/itkLabelMapToBinaryImageFilter.txx b/Utilities/InsightJournal/itkLabelMapToBinaryImageFilter.txx
deleted file mode 100644
index f9ba51ab8dd2bf6ae42caabf640cb06ba80b4aa7..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkLabelMapToBinaryImageFilter.txx
+++ /dev/null
@@ -1,147 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkLabelMapToBinaryImageFilter.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 __itkLabelMapToBinaryImageFilter_txx
-#define __itkLabelMapToBinaryImageFilter_txx
-
-#include "itkLabelMapToBinaryImageFilter.h"
-#include "itkNumericTraits.h"
-#include "itkProgressReporter.h"
-#include "itkImageRegionConstIterator.h"
-#include "itkImageRegionIterator.h"
-
-namespace itk {
-
-template <class TInputImage, class TOutputImage>
-LabelMapToBinaryImageFilter<TInputImage, TOutputImage>
-::LabelMapToBinaryImageFilter()
-{
- m_BackgroundValue = NumericTraits<OutputImagePixelType>::NonpositiveMin();
- m_ForegroundValue = NumericTraits<OutputImagePixelType>::max();
-}
-
-template <class TInputImage, class TOutputImage>
-void
-LabelMapToBinaryImageFilter<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
-LabelMapToBinaryImageFilter<TInputImage, TOutputImage>
-::EnlargeOutputRequestedRegion(DataObject *)
-{
- this->GetOutput()
- ->SetRequestedRegion( this->GetOutput()->GetLargestPossibleRegion() );
-}
-
-
-template<class TInputImage, class TOutputImage>
-void
-LabelMapToBinaryImageFilter<TInputImage, TOutputImage>
-::BeforeThreadedGenerateData()
-{
- m_Barrier = Barrier::New();
- m_Barrier->Initialize( this->GetNumberOfThreads() );
-
- Superclass::BeforeThreadedGenerateData();
-
-}
-
-
-template<class TInputImage, class TOutputImage>
-void
-LabelMapToBinaryImageFilter<TInputImage, TOutputImage>
-::ThreadedGenerateData( const OutputImageRegionType& outputRegionForThread, int threadId )
-{
- OutputImageType * output = this->GetOutput();
-// const InputImageType * input = this->GetInput();
-
- // fill the output with background value - they will be overiden with the foreground value
- // later, if there is some objects
- if( this->GetNumberOfInputs() == 2 )
- {
- // fill the background with the background values from the background image
- ImageRegionConstIterator< OutputImageType > bgIt( this->GetBackgroundImage(), outputRegionForThread );
- ImageRegionIterator< OutputImageType > oIt( output, outputRegionForThread );
- for( oIt.GoToBegin(), bgIt.GoToBegin();
- !oIt.IsAtEnd();
- ++oIt, ++bgIt )
- {
- const OutputImagePixelType & bg = bgIt.Get();
- if( bg != m_ForegroundValue )
- {
- oIt.Set( bg );
- }
- else
- {
- oIt.Set( m_BackgroundValue );
- }
- }
- }
- else
- {
- // fill the background with the background value
- ImageRegionIterator< OutputImageType > oIt( output, outputRegionForThread );
- for( oIt.GoToBegin(); !oIt.IsAtEnd(); ++oIt )
- {
- oIt.Set( m_BackgroundValue );
- }
- }
-
- // 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 TOutputImage>
-void
-LabelMapToBinaryImageFilter<TInputImage, TOutputImage>
-::ThreadedGenerateData( LabelObjectType * labelObject )
-{
- OutputImageType * output = this->GetOutput();
-
- 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, m_ForegroundValue );
- idx[0]++;
- }
- }
-}
-
-}// end namespace itk
-#endif
diff --git a/Utilities/InsightJournal/itkLabelMapToLabelImageFilter.h b/Utilities/InsightJournal/itkLabelMapToLabelImageFilter.h
deleted file mode 100644
index f39b84ddf7cfbaa3b7b1c5c94878c66413d2d268..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkLabelMapToLabelImageFilter.h
+++ /dev/null
@@ -1,96 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkLabelMapToLabelImageFilter.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 __itkLabelMapToLabelImageFilter_h
-#define __itkLabelMapToLabelImageFilter_h
-
-#include "itkLabelMapFilter.h"
-
-namespace itk {
-
-/** \class LabelMapToLabelImageFilter
- * \brief Convert a LabelMap to a labeled image
- *
- * LabelMapToBinaryImageFilter to a label 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>
-class ITK_EXPORT LabelMapToLabelImageFilter :
- public LabelMapFilter<TInputImage, TOutputImage>
-{
-public:
- /** Standard class typedefs. */
- typedef LabelMapToLabelImageFilter 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;
-
- /** ImageDimension constants */
- itkStaticConstMacro(InputImageDimension, unsigned int,
- TInputImage::ImageDimension);
- itkStaticConstMacro(OutputImageDimension, unsigned int,
- TOutputImage::ImageDimension);
-
- /** Standard New method. */
- itkNewMacro(Self);
-
- /** Runtime information support. */
- itkTypeMacro(LabelMapToLabelImageFilter,
- ImageToImageFilter);
-
-protected:
- LabelMapToLabelImageFilter();
- ~LabelMapToLabelImageFilter() {};
-
- virtual void BeforeThreadedGenerateData();
-
- virtual void ThreadedGenerateData( LabelObjectType * labelObject );
-
-private:
- LabelMapToLabelImageFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
-} ; // end of class
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkLabelMapToLabelImageFilter.txx"
-#endif
-
-#endif
-
-
diff --git a/Utilities/InsightJournal/itkLabelMapToLabelImageFilter.txx b/Utilities/InsightJournal/itkLabelMapToLabelImageFilter.txx
deleted file mode 100644
index f2e564180a02f9cd4ed5eac2ae595dcf0667d7cf..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkLabelMapToLabelImageFilter.txx
+++ /dev/null
@@ -1,72 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkLabelMapToLabelImageFilter.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 __itkLabelMapToLabelImageFilter_txx
-#define __itkLabelMapToLabelImageFilter_txx
-
-#include "itkLabelMapToLabelImageFilter.h"
-#include "itkNumericTraits.h"
-#include "itkProgressReporter.h"
-#include "itkImageRegionConstIteratorWithIndex.h"
-
-namespace itk {
-
-template <class TInputImage, class TOutputImage>
-LabelMapToLabelImageFilter<TInputImage, TOutputImage>
-::LabelMapToLabelImageFilter()
-{
-}
-
-
-template<class TInputImage, class TOutputImage>
-void
-LabelMapToLabelImageFilter<TInputImage, TOutputImage>
-::BeforeThreadedGenerateData()
-{
- OutputImageType * output = this->GetOutput();
- const InputImageType * input = this->GetInput();
-
- output->FillBuffer( input->GetBackgroundValue() );
-
- Superclass::BeforeThreadedGenerateData();
-
-}
-
-
-template<class TInputImage, class TOutputImage>
-void
-LabelMapToLabelImageFilter<TInputImage, TOutputImage>
-::ThreadedGenerateData( LabelObjectType * labelObject )
-{
- const typename LabelObjectType::LabelType & label = labelObject->GetLabel();
-
- 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, label );
- idx[0]++;
- }
- }
-}
-
-}// end namespace itk
-#endif
diff --git a/Utilities/InsightJournal/itkLabelPerimeterEstimationCalculator.h b/Utilities/InsightJournal/itkLabelPerimeterEstimationCalculator.h
deleted file mode 100644
index 9e69defa7880c691d39b9b26b3ae931dc0090b03..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkLabelPerimeterEstimationCalculator.h
+++ /dev/null
@@ -1,121 +0,0 @@
-#ifndef __itkLabelPerimeterEstimationCalculator_h
-#define __itkLabelPerimeterEstimationCalculator_h
-
-#include "itkObject.h"
-
-namespace itk {
-
-/** \class LabelPerimeterEstimationCalculator
- * \brief TODO
- *
- * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
- *
- * \sa
- */
-template<class TInputImage>
-class ITK_EXPORT LabelPerimeterEstimationCalculator :
- public Object
-{
-public:
- /** Standard class typedefs. */
- typedef LabelPerimeterEstimationCalculator Self;
- typedef Object 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::RegionType RegionType;
- typedef typename InputImageType::SizeType SizeType;
- typedef typename InputImageType::IndexType IndexType;
-
- typedef typename std::map< InputImagePixelType, double > PerimetersType;
-
- /** ImageDimension constants */
- itkStaticConstMacro(ImageDimension, unsigned int,
- TInputImage::ImageDimension);
-
- /** Standard New method. */
- itkNewMacro(Self);
-
- /** Runtime information support. */
- itkTypeMacro(LabelPerimeterEstimationCalculator,
- Object);
-
- /**
- * 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);
-
- void SetImage( const InputImageType * img )
- {
- m_Image = img;
- }
-
- const InputImageType * GetImage() const
- {
- return m_Image;
- }
-
- void Compute();
-
- const PerimetersType & GetPerimeters() const
- {
- return m_Perimeters;
- }
-
- const double & GetPerimeter( const InputImagePixelType & label ) const
- {
- if( m_Perimeters.find( label ) != m_Perimeters.end() )
- {
- return m_Perimeters.find( label )->second;
- }
- itkExceptionMacro( << "Unknown label: " << static_cast<typename NumericTraits<InputImagePixelType>::PrintType>(label) );
- }
-
- bool HasLabel( const InputImagePixelType & label ) const
- {
- if( m_Perimeters.find( label ) != m_Perimeters.end() )
- {
- return true;
- }
- return false;
- }
-
-protected:
- LabelPerimeterEstimationCalculator();
- ~LabelPerimeterEstimationCalculator() {};
- void PrintSelf(std::ostream& os, Indent indent) const;
-
-
-private:
- LabelPerimeterEstimationCalculator(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
- bool m_FullyConnected;
-
- const InputImageType * m_Image;
-
- PerimetersType m_Perimeters;
-
-} ; // end of class
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkLabelPerimeterEstimationCalculator.txx"
-#endif
-
-#endif
-
-
diff --git a/Utilities/InsightJournal/itkLabelPerimeterEstimationCalculator.txx b/Utilities/InsightJournal/itkLabelPerimeterEstimationCalculator.txx
deleted file mode 100644
index 5b4e13c01ad5fb5d14a83e79cccdd05806c18f7e..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkLabelPerimeterEstimationCalculator.txx
+++ /dev/null
@@ -1,236 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkLabelPerimeterEstimationCalculator.txx,v $
- Language: C++
- Date: $Date: 2004/12/21 22:47:30 $
- Version: $Revision: 1.12 $
-
- 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 __itkLabelPerimeterEstimationCalculator_txx
-#define __itkLabelPerimeterEstimationCalculator_txx
-
-#include "itkLabelPerimeterEstimationCalculator.h"
-#include "itkProgressReporter.h"
-#include "itkImageRegionIterator.h"
-#include "itkImageRegionConstIteratorWithIndex.h"
-#include "itkShapedNeighborhoodIterator.h"
-#include "itkConstShapedNeighborhoodIterator.h"
-#include "itkConstantBoundaryCondition.h"
-#include "itkSize.h"
-#include "itkConnectedComponentAlgorithm.h"
-#include <set>
-
-namespace itk {
-
-template <class TInputImage>
-LabelPerimeterEstimationCalculator<TInputImage>
-::LabelPerimeterEstimationCalculator()
-{
- m_FullyConnected = false;
-}
-
-
-
-template<class TInputImage>
-void
-LabelPerimeterEstimationCalculator<TInputImage>
-::Compute()
-{
-
- m_Perimeters.clear();
-
- // ProgressReporter progress( this, 0, this->GetImage()->GetRequestedRegion().GetNumberOfPixels() );
-
- // reduce the region to avoid reading outside
- RegionType region = this->GetImage()->GetRequestedRegion();
- SizeType size = region.GetSize();
- for( int i=0; i<ImageDimension; i++ )
- {
- size[i]--;
- }
- region.SetSize( size );
-
- // the radius which will be used for all the shaped iterators
- Size< ImageDimension > radius;
- radius.Fill(1);
-
- // set up the iterator
- typedef ConstShapedNeighborhoodIterator<InputImageType> IteratorType;
- typename IteratorType::ConstIterator nIt;
- IteratorType iIt( radius, this->GetImage(), region );
-// ConstantBoundaryCondition<InputImageType> lcbc;
-// lcbc.SetConstant( NumericTraits<InputImagePixelType>::max() );
-// iIt.OverrideBoundaryCondition(&lcbc);
- // we want to search the neighbors with offset >= 0
- // 2D -> 4 neighbors
- // 3D -> 8 neighbors
- typename IteratorType::OffsetType offset;
- unsigned int centerIndex = iIt.GetCenterNeighborhoodIndex();
- // store the offsets to reuse them to evaluate the contributions of the
- // configurations
- typename std::vector< IndexType > indexes;
- IndexType idx0;
- idx0.Fill( 0 );
- for( unsigned int d=centerIndex; d < 2*centerIndex+1; d++ )
- {
- offset = iIt.GetOffset( d );
- bool deactivate = false;
- for ( int j=0; j<ImageDimension && !deactivate; j++ )
- {
- if( offset[j] < 0 )
- {
- deactivate = true;
- }
- }
- if( deactivate )
- {
-// std::cout << "- " << offset << std::endl;
- iIt.DeactivateOffset( offset );
- }
- else
- {
-// std::cout << "+ " << idx0 + offset << std::endl;
- iIt.ActivateOffset( offset );
- indexes.push_back( idx0 + offset );
- }
-
- }
-
- // to store the configurations count for all the labels
- typedef typename std::map< unsigned long, unsigned long > MapType;
- typedef typename std::map< InputImagePixelType, MapType > LabelMapType;
- LabelMapType confCount;
-
- for( iIt.GoToBegin(); !iIt.IsAtEnd(); ++iIt )
- {
- // 2 pass - find the labels in the neighborhood
- // - count the configurations for all the labels
-
- typedef typename std::set< InputImagePixelType > LabelSetType;
- LabelSetType labelSet;
- for ( nIt= iIt.Begin();
- nIt != iIt.End();
- nIt++ )
- {
- labelSet.insert( nIt.Get() );
- }
-
- for( typename LabelSetType::const_iterator it=labelSet.begin();
- it!=labelSet.end();
- it++ )
- {
-
- unsigned long conf = 0;
- int i=0;
-
- for ( nIt= iIt.Begin();
- nIt != iIt.End();
- nIt++, i++ )
- {
- if( nIt.Get() == *it )
- {
- conf += 1 << i;
- }
- }
-
- confCount[ *it ][ conf ]++;
-
- }
-
- // progress.CompletedPixel();
-
- }
-
- // compute the participation to the perimeter for all the configurations
-// std::cout << "spacing: " << this->GetImage()->GetSpacing() << std::endl;
- double physicalSize = 1;
- for( int i=0; i<ImageDimension; i++ )
- {
- physicalSize *= this->GetImage()->GetSpacing()[i];
- }
- typedef typename std::map< unsigned long, double > ContributionMapType;
- ContributionMapType contributions;
- int numberOfNeighbors = (int)vcl_pow( 2.0, ImageDimension );
- int numberOfConfigurations = (int)vcl_pow( 2.0, numberOfNeighbors );
- // create an image to store the neighbors
- typedef typename itk::Image< bool, ImageDimension > ImageType;
- typename ImageType::Pointer neighborsImage = ImageType::New();
- // typename ImageType::SizeType size;
- size.Fill( 2 );
- neighborsImage->SetRegions( size );
- neighborsImage->Allocate();
- for( int i=0; i<numberOfConfigurations; i++ )
- {
- neighborsImage->FillBuffer( false );
- for( int j=0; j<numberOfNeighbors; j++ )
- {
- if( i & 1 << j )
- {
- neighborsImage->SetPixel( indexes[ j ], true );
- }
- }
- // the image is created - we can now compute the contributions of the pixels
- // for that configuration
- contributions[i] = 0;
- for( int j=0; j<numberOfNeighbors; j++ )
- {
- IndexType currentIdx = indexes[j];
- if( neighborsImage->GetPixel( currentIdx ) )
- {
- for( int k=0; k<ImageDimension; k++ )
- {
- IndexType idx = currentIdx;
- idx[k] = vcl_abs( idx[k] - 1 );
- if( !neighborsImage->GetPixel( idx ) )
- {
- contributions[i] += physicalSize / this->GetImage()->GetSpacing()[k] / 2.0;
- }
- }
- }
- }
- contributions[i] /= ImageDimension;
-// std::cout << "configuration: " << i << " contribution: " << contributions[i] << std::endl;
- }
-
-
- // and use those contributions to found the perimeter
- m_Perimeters.clear();
- for( typename LabelMapType::const_iterator it=confCount.begin();
- it!=confCount.end();
- it++ )
- {
- m_Perimeters[ it->first ] = 0;
- for( typename MapType::const_iterator it2=it->second.begin();
- it2!=it->second.end();
- it2++ )
- {
- m_Perimeters[ it->first ] += contributions[ it2->first ] * it2->second;
-// std::cout << it->first+0.0 << " " << it2->first << " " << it2->second << std::endl;
- }
-// std::cout << "label: " << it->first+0.0 << " perimeter: " << m_Perimeters[ it->first ] << std::endl;
- }
-
-}
-
-
-
-template<class TInputImage>
-void
-LabelPerimeterEstimationCalculator<TInputImage>
-::PrintSelf(std::ostream &os, Indent indent) const
-{
- Superclass::PrintSelf(os, indent);
-
- os << indent << "FullyConnected: " << m_FullyConnected << std::endl;
-}
-
-}// end namespace itk
-#endif
diff --git a/Utilities/InsightJournal/itkLabelShapeKeepNObjectsImageFilter.h b/Utilities/InsightJournal/itkLabelShapeKeepNObjectsImageFilter.h
deleted file mode 100644
index a778dd6b4dfd9203b22de6e7ac18c6943f0e4a32..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkLabelShapeKeepNObjectsImageFilter.h
+++ /dev/null
@@ -1,170 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkLabelShapeKeepNObjectsImageFilter.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 __itkLabelShapeKeepNObjectsImageFilter_h
-#define __itkLabelShapeKeepNObjectsImageFilter_h
-
-#include "itkImageToImageFilter.h"
-#include "itkShapeLabelObject.h"
-#include "itkLabelMap.h"
-#include "itkLabelImageToLabelMapFilter.h"
-#include "itkShapeLabelMapFilter.h"
-#include "itkShapeKeepNObjectsLabelMapFilter.h"
-#include "itkLabelMapToLabelImageFilter.h"
-
-
-namespace itk {
-
-/** \class LabelShapeKeepNObjectsImageFilter
- * \brief keep N objects according to their shape attributes
- *
- * LabelShapeKeepNObjectsImageFilter keep the N objects in a labeled 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, BinaryShapeKeepNObjectsImageFilter, LabelStatisticsKeepNObjectsImageFilter
- * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
- */
-template<class TInputImage>
-class ITK_EXPORT LabelShapeKeepNObjectsImageFilter :
- public ImageToImageFilter<TInputImage, TInputImage>
-{
-public:
- /** Standard class typedefs. */
- typedef LabelShapeKeepNObjectsImageFilter 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<InputImagePixelType, ImageDimension> LabelObjectType;
- typedef typename itk::LabelMap< LabelObjectType > LabelMapType;
- typedef typename itk::LabelImageToLabelMapFilter< InputImageType, LabelMapType > LabelizerType;
- typedef typename itk::ShapeLabelMapFilter< LabelMapType > LabelObjectValuatorType;
- typedef typename LabelObjectType::AttributeType AttributeType;
- typedef typename itk::ShapeKeepNObjectsLabelMapFilter< LabelMapType > KeepNObjectsType;
- typedef typename itk::LabelMapToLabelImageFilter< LabelMapType, OutputImageType > BinarizerType;
-
- /** Standard New method. */
- itkNewMacro(Self);
-
- /** Runtime information support. */
- itkTypeMacro(LabelShapeKeepNObjectsImageFilter,
- 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 );
-
- /**
- * 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:
- LabelShapeKeepNObjectsImageFilter();
- ~LabelShapeKeepNObjectsImageFilter() {};
- void PrintSelf(std::ostream& os, Indent indent) const;
-
- /** LabelShapeKeepNObjectsImageFilter needs the entire input be
- * available. Thus, it needs to provide an implementation of
- * GenerateInputRequestedRegion(). */
- void GenerateInputRequestedRegion() ;
-
- /** LabelShapeKeepNObjectsImageFilter will produce the entire output. */
- void EnlargeOutputRequestedRegion(DataObject *itkNotUsed(output));
-
- /** Single-threaded version of GenerateData. This filter delegates
- * to GrayscaleGeodesicErodeImageFilter. */
- void GenerateData();
-
-private:
- LabelShapeKeepNObjectsImageFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
- OutputImagePixelType m_BackgroundValue;
- unsigned long m_NumberOfObjects;
- bool m_ReverseOrdering;
- AttributeType m_Attribute;
-} ; // end of class
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkLabelShapeKeepNObjectsImageFilter.txx"
-#endif
-
-#endif
-
-
diff --git a/Utilities/InsightJournal/itkLabelShapeKeepNObjectsImageFilter.txx b/Utilities/InsightJournal/itkLabelShapeKeepNObjectsImageFilter.txx
deleted file mode 100644
index 1c061ba8e595a36cd839731eb2406d09e5bfb10a..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkLabelShapeKeepNObjectsImageFilter.txx
+++ /dev/null
@@ -1,128 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkLabelShapeKeepNObjectsImageFilter.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 __itkLabelShapeKeepNObjectsImageFilter_txx
-#define __itkLabelShapeKeepNObjectsImageFilter_txx
-
-#include "itkLabelShapeKeepNObjectsImageFilter.h"
-#include "itkProgressAccumulator.h"
-
-
-namespace itk {
-
-template<class TInputImage>
-LabelShapeKeepNObjectsImageFilter<TInputImage>
-::LabelShapeKeepNObjectsImageFilter()
-{
- m_BackgroundValue = NumericTraits<OutputImagePixelType>::NonpositiveMin();
- m_NumberOfObjects = 1;
- m_ReverseOrdering = false;
- m_Attribute = LabelObjectType::SIZE;
-}
-
-template<class TInputImage>
-void
-LabelShapeKeepNObjectsImageFilter<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
-LabelShapeKeepNObjectsImageFilter<TInputImage>
-::EnlargeOutputRequestedRegion(DataObject *)
-{
- this->GetOutput()
- ->SetRequestedRegion( this->GetOutput()->GetLargestPossibleRegion() );
-}
-
-
-template<class TInputImage>
-void
-LabelShapeKeepNObjectsImageFilter<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->SetBackgroundValue( m_BackgroundValue );
- labelizer->SetNumberOfThreads( this->GetNumberOfThreads() );
- progress->RegisterInternalFilter(labelizer, .3f);
-
- typename LabelObjectValuatorType::Pointer valuator = LabelObjectValuatorType::New();
- valuator->SetInput( labelizer->GetOutput() );
- valuator->SetLabelImage( this->GetInput() );
- 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->SetNumberOfThreads( this->GetNumberOfThreads() );
- progress->RegisterInternalFilter(binarizer, .2f);
-
- binarizer->GraftOutput( this->GetOutput() );
- binarizer->Update();
- this->GraftOutput( binarizer->GetOutput() );
-}
-
-
-template<class TInputImage>
-void
-LabelShapeKeepNObjectsImageFilter<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;
- 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/itkLabelShapeOpeningImageFilter.h b/Utilities/InsightJournal/itkLabelShapeOpeningImageFilter.h
deleted file mode 100644
index e58824fb3c630c69fdcfba7ba83aa01c632f32a6..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkLabelShapeOpeningImageFilter.h
+++ /dev/null
@@ -1,172 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkLabelShapeOpeningImageFilter.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 __itkLabelShapeOpeningImageFilter_h
-#define __itkLabelShapeOpeningImageFilter_h
-
-#include "itkImageToImageFilter.h"
-#include "itkShapeLabelObject.h"
-#include "itkLabelMap.h"
-#include "itkLabelImageToLabelMapFilter.h"
-#include "itkShapeLabelMapFilter.h"
-#include "itkShapeOpeningLabelMapFilter.h"
-#include "itkLabelMapToLabelImageFilter.h"
-
-
-namespace itk {
-
-/** \class LabelShapeOpeningImageFilter
- * \brief remove the objects according to the value of their shape attribute
- *
- * LabelShapeOpeningImageFilter removes the objects in a labeled 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, BinaryShapeOpeningImageFilter, LabelStatisticsOpeningImageFilter
- * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
- */
-template<class TInputImage>
-class ITK_EXPORT LabelShapeOpeningImageFilter :
- public ImageToImageFilter<TInputImage, TInputImage>
-{
-public:
- /** Standard class typedefs. */
- typedef LabelShapeOpeningImageFilter 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<InputImagePixelType, ImageDimension> LabelObjectType;
- typedef typename itk::LabelMap< LabelObjectType > LabelMapType;
- typedef typename itk::LabelImageToLabelMapFilter< InputImageType, LabelMapType > LabelizerType;
- typedef typename itk::ShapeLabelMapFilter< LabelMapType > LabelObjectValuatorType;
- typedef typename LabelObjectType::AttributeType AttributeType;
- typedef typename itk::ShapeOpeningLabelMapFilter< LabelMapType > OpeningType;
- typedef typename itk::LabelMapToLabelImageFilter< LabelMapType, OutputImageType > BinarizerType;
-
- /** Standard New method. */
- itkNewMacro(Self);
-
- /** Runtime information support. */
- itkTypeMacro(LabelShapeOpeningImageFilter,
- 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, 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:
- LabelShapeOpeningImageFilter();
- ~LabelShapeOpeningImageFilter() {};
- void PrintSelf(std::ostream& os, Indent indent) const;
-
- /** LabelShapeOpeningImageFilter needs the entire input be
- * available. Thus, it needs to provide an implementation of
- * GenerateInputRequestedRegion(). */
- void GenerateInputRequestedRegion() ;
-
- /** LabelShapeOpeningImageFilter will produce the entire output. */
- void EnlargeOutputRequestedRegion(DataObject *itkNotUsed(output));
-
- /** Single-threaded version of GenerateData. This filter delegates
- * to GrayscaleGeodesicErodeImageFilter. */
- void GenerateData();
-
-
-private:
- LabelShapeOpeningImageFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
- OutputImagePixelType m_BackgroundValue;
- double m_Lambda;
- bool m_ReverseOrdering;
- AttributeType m_Attribute;
-} ; // end of class
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkLabelShapeOpeningImageFilter.txx"
-#endif
-
-#endif
-
-
diff --git a/Utilities/InsightJournal/itkLabelShapeOpeningImageFilter.txx b/Utilities/InsightJournal/itkLabelShapeOpeningImageFilter.txx
deleted file mode 100644
index d763a167bbc3c7cdd7640b2557275b3450a1dc3d..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkLabelShapeOpeningImageFilter.txx
+++ /dev/null
@@ -1,128 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkLabelShapeOpeningImageFilter.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 __itkLabelShapeOpeningImageFilter_txx
-#define __itkLabelShapeOpeningImageFilter_txx
-
-#include "itkLabelShapeOpeningImageFilter.h"
-#include "itkProgressAccumulator.h"
-
-
-namespace itk {
-
-template<class TInputImage>
-LabelShapeOpeningImageFilter<TInputImage>
-::LabelShapeOpeningImageFilter()
-{
- m_BackgroundValue = NumericTraits<OutputImagePixelType>::NonpositiveMin();
- m_Lambda = NumericTraits< double >::Zero;
- m_ReverseOrdering = false;
- m_Attribute = LabelObjectType::SIZE;
-}
-
-template<class TInputImage>
-void
-LabelShapeOpeningImageFilter<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
-LabelShapeOpeningImageFilter<TInputImage>
-::EnlargeOutputRequestedRegion(DataObject *)
-{
- this->GetOutput()
- ->SetRequestedRegion( this->GetOutput()->GetLargestPossibleRegion() );
-}
-
-
-template<class TInputImage>
-void
-LabelShapeOpeningImageFilter<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->SetBackgroundValue( m_BackgroundValue );
- labelizer->SetNumberOfThreads( this->GetNumberOfThreads() );
- progress->RegisterInternalFilter(labelizer, .3f);
-
- typename LabelObjectValuatorType::Pointer valuator = LabelObjectValuatorType::New();
- valuator->SetInput( labelizer->GetOutput() );
- valuator->SetLabelImage( this->GetInput() );
- 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->SetNumberOfThreads( this->GetNumberOfThreads() );
- progress->RegisterInternalFilter(binarizer, .2f);
-
- binarizer->GraftOutput( this->GetOutput() );
- binarizer->Update();
- this->GraftOutput( binarizer->GetOutput() );
-}
-
-
-template<class TInputImage>
-void
-LabelShapeOpeningImageFilter<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;
- 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/itkLabelStatisticsKeepNObjectsImageFilter.h b/Utilities/InsightJournal/itkLabelStatisticsKeepNObjectsImageFilter.h
deleted file mode 100644
index 4d601c477dedc91c792e84096c976fa21e4a9836..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkLabelStatisticsKeepNObjectsImageFilter.h
+++ /dev/null
@@ -1,200 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkLabelStatisticsKeepNObjectsImageFilter.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 __itkLabelStatisticsKeepNObjectsImageFilter_h
-#define __itkLabelStatisticsKeepNObjectsImageFilter_h
-
-#include "itkImageToImageFilter.h"
-#include "itkStatisticsLabelObject.h"
-#include "itkLabelMap.h"
-#include "itkLabelImageToLabelMapFilter.h"
-#include "itkStatisticsLabelMapFilter.h"
-#include "itkStatisticsKeepNObjectsLabelMapFilter.h"
-#include "itkLabelMapToLabelImageFilter.h"
-
-
-namespace itk {
-
-/** \class LabelStatisticsKeepNObjectsImageFilter
- * \brief keep N objects according to their statistics attributes
- *
- * LabelStatisticsKeepNObjectsImageFilter keep the N objects in a labeled 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, BinaryStatisticsKeepNObjectsImageFilter, LabelShapeKeepNObjectsImageFilter
- * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
- */
-template<class TInputImage, class TFeatureImage>
-class ITK_EXPORT LabelStatisticsKeepNObjectsImageFilter :
- public ImageToImageFilter<TInputImage, TInputImage>
-{
-public:
- /** Standard class typedefs. */
- typedef LabelStatisticsKeepNObjectsImageFilter 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<InputImagePixelType, ImageDimension> LabelObjectType;
- typedef typename itk::LabelMap< LabelObjectType > LabelMapType;
- typedef typename itk::LabelImageToLabelMapFilter< InputImageType, LabelMapType > LabelizerType;
- typedef typename itk::StatisticsLabelMapFilter< LabelMapType, TFeatureImage > LabelObjectValuatorType;
- typedef typename LabelObjectType::AttributeType AttributeType;
- typedef typename itk::StatisticsKeepNObjectsLabelMapFilter< LabelMapType > KeepNObjectsType;
- typedef typename itk::LabelMapToLabelImageFilter< LabelMapType, OutputImageType > BinarizerType;
-
- /** Standard New method. */
- itkNewMacro(Self);
-
- /** Runtime information support. */
- itkTypeMacro(LabelStatisticsKeepNObjectsImageFilter,
- 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 );
-
- /**
- * 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:
- LabelStatisticsKeepNObjectsImageFilter();
- ~LabelStatisticsKeepNObjectsImageFilter() {};
- void PrintSelf(std::ostream& os, Indent indent) const;
-
- /** LabelStatisticsKeepNObjectsImageFilter needs the entire input be
- * available. Thus, it needs to provide an implementation of
- * GenerateInputRequestedRegion(). */
- void GenerateInputRequestedRegion() ;
-
- /** LabelStatisticsKeepNObjectsImageFilter will produce the entire output. */
- void EnlargeOutputRequestedRegion(DataObject *itkNotUsed(output));
-
- /** Single-threaded version of GenerateData. This filter delegates
- * to GrayscaleGeodesicErodeImageFilter. */
- void GenerateData();
-
-private:
- LabelStatisticsKeepNObjectsImageFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
- OutputImagePixelType m_BackgroundValue;
- unsigned long m_NumberOfObjects;
- bool m_ReverseOrdering;
- AttributeType m_Attribute;
-} ; // end of class
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkLabelStatisticsKeepNObjectsImageFilter.txx"
-#endif
-
-#endif
-
-
diff --git a/Utilities/InsightJournal/itkLabelStatisticsKeepNObjectsImageFilter.txx b/Utilities/InsightJournal/itkLabelStatisticsKeepNObjectsImageFilter.txx
deleted file mode 100644
index dc7c4f75a69b383b417254a032fe35f5da85ad9b..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkLabelStatisticsKeepNObjectsImageFilter.txx
+++ /dev/null
@@ -1,131 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkLabelStatisticsKeepNObjectsImageFilter.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 __itkLabelStatisticsKeepNObjectsImageFilter_txx
-#define __itkLabelStatisticsKeepNObjectsImageFilter_txx
-
-#include "itkLabelStatisticsKeepNObjectsImageFilter.h"
-#include "itkProgressAccumulator.h"
-
-
-namespace itk {
-
-template<class TInputImage, class TFeatureImage>
-LabelStatisticsKeepNObjectsImageFilter<TInputImage, TFeatureImage>
-::LabelStatisticsKeepNObjectsImageFilter()
-{
- m_BackgroundValue = NumericTraits<OutputImagePixelType>::NonpositiveMin();
- m_NumberOfObjects = 1;
- m_ReverseOrdering = false;
- m_Attribute = LabelObjectType::MEAN;
- this->SetNumberOfRequiredInputs(2);
-}
-
-template<class TInputImage, class TFeatureImage>
-void
-LabelStatisticsKeepNObjectsImageFilter<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
-LabelStatisticsKeepNObjectsImageFilter<TInputImage, TFeatureImage>
-::EnlargeOutputRequestedRegion(DataObject *)
-{
- this->GetOutput()
- ->SetRequestedRegion( this->GetOutput()->GetLargestPossibleRegion() );
-}
-
-
-template<class TInputImage, class TFeatureImage>
-void
-LabelStatisticsKeepNObjectsImageFilter<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->SetBackgroundValue( m_BackgroundValue );
- labelizer->SetNumberOfThreads( this->GetNumberOfThreads() );
- progress->RegisterInternalFilter(labelizer, .3f);
-
- typename LabelObjectValuatorType::Pointer valuator = LabelObjectValuatorType::New();
- valuator->SetInput( labelizer->GetOutput() );
- valuator->SetFeatureImage( this->GetFeatureImage() );
- valuator->SetLabelImage( this->GetInput() );
- 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->SetNumberOfThreads( this->GetNumberOfThreads() );
- progress->RegisterInternalFilter(binarizer, .2f);
-
- binarizer->GraftOutput( this->GetOutput() );
- binarizer->Update();
- this->GraftOutput( binarizer->GetOutput() );
-}
-
-
-template<class TInputImage, class TFeatureImage>
-void
-LabelStatisticsKeepNObjectsImageFilter<TInputImage, TFeatureImage>
-::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;
- os << indent << "Attribute: " << LabelObjectType::GetNameFromAttribute(m_Attribute) << " (" << m_Attribute << ")" << std::endl;
-}
-
-}// end namespace itk
-#endif
diff --git a/Utilities/InsightJournal/itkLabelStatisticsOpeningImageFilter.h b/Utilities/InsightJournal/itkLabelStatisticsOpeningImageFilter.h
deleted file mode 100644
index 3adec7082e5b92e841249d8551270bb06436605a..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkLabelStatisticsOpeningImageFilter.h
+++ /dev/null
@@ -1,202 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkLabelStatisticsOpeningImageFilter.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 __itkLabelStatisticsOpeningImageFilter_h
-#define __itkLabelStatisticsOpeningImageFilter_h
-
-#include "itkImageToImageFilter.h"
-#include "itkStatisticsLabelObject.h"
-#include "itkLabelMap.h"
-#include "itkLabelImageToLabelMapFilter.h"
-#include "itkStatisticsLabelMapFilter.h"
-#include "itkStatisticsOpeningLabelMapFilter.h"
-#include "itkLabelMapToLabelImageFilter.h"
-
-
-namespace itk {
-
-/** \class LabelStatisticsOpeningImageFilter
- * \brief remove the objects according to the value of their statistics attribute
- *
- * LabelStatisticsOpeningImageFilter removes the objects in a labeled 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, BinaryStatisticsOpeningImageFilter, LabelShapeOpeningImageFilter
- * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
- */
-template<class TInputImage, class TFeatureImage>
-class ITK_EXPORT LabelStatisticsOpeningImageFilter :
- public ImageToImageFilter<TInputImage, TInputImage>
-{
-public:
- /** Standard class typedefs. */
- typedef LabelStatisticsOpeningImageFilter 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<InputImagePixelType, ImageDimension> LabelObjectType;
- typedef typename itk::LabelMap< LabelObjectType > LabelMapType;
- typedef typename itk::LabelImageToLabelMapFilter< InputImageType, LabelMapType > LabelizerType;
- typedef typename itk::StatisticsLabelMapFilter< LabelMapType, TFeatureImage > LabelObjectValuatorType;
- typedef typename LabelObjectType::AttributeType AttributeType;
- typedef typename itk::StatisticsOpeningLabelMapFilter< LabelMapType > OpeningType;
- typedef typename itk::LabelMapToLabelImageFilter< LabelMapType, OutputImageType > BinarizerType;
-
- /** Standard New method. */
- itkNewMacro(Self);
-
- /** Runtime information support. */
- itkTypeMacro(LabelStatisticsOpeningImageFilter,
- 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, 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:
- LabelStatisticsOpeningImageFilter();
- ~LabelStatisticsOpeningImageFilter() {};
- void PrintSelf(std::ostream& os, Indent indent) const;
-
- /** LabelStatisticsOpeningImageFilter needs the entire input be
- * available. Thus, it needs to provide an implementation of
- * GenerateInputRequestedRegion(). */
- void GenerateInputRequestedRegion() ;
-
- /** LabelStatisticsOpeningImageFilter will produce the entire output. */
- void EnlargeOutputRequestedRegion(DataObject *itkNotUsed(output));
-
- /** Single-threaded version of GenerateData. This filter delegates
- * to GrayscaleGeodesicErodeImageFilter. */
- void GenerateData();
-
-
-private:
- LabelStatisticsOpeningImageFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
- OutputImagePixelType m_BackgroundValue;
- double m_Lambda;
- bool m_ReverseOrdering;
- AttributeType m_Attribute;
-} ; // end of class
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkLabelStatisticsOpeningImageFilter.txx"
-#endif
-
-#endif
-
-
diff --git a/Utilities/InsightJournal/itkLabelStatisticsOpeningImageFilter.txx b/Utilities/InsightJournal/itkLabelStatisticsOpeningImageFilter.txx
deleted file mode 100644
index 008b0abf2fbcebd1df2c7018ee0856209856e93a..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkLabelStatisticsOpeningImageFilter.txx
+++ /dev/null
@@ -1,131 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkLabelStatisticsOpeningImageFilter.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 __itkLabelStatisticsOpeningImageFilter_txx
-#define __itkLabelStatisticsOpeningImageFilter_txx
-
-#include "itkLabelStatisticsOpeningImageFilter.h"
-#include "itkProgressAccumulator.h"
-
-
-namespace itk {
-
-template<class TInputImage, class TFeatureImage>
-LabelStatisticsOpeningImageFilter<TInputImage, TFeatureImage>
-::LabelStatisticsOpeningImageFilter()
-{
- m_BackgroundValue = NumericTraits<OutputImagePixelType>::NonpositiveMin();
- m_Lambda = NumericTraits< double >::Zero;
- m_ReverseOrdering = false;
- m_Attribute = LabelObjectType::MEAN;
- this->SetNumberOfRequiredInputs(2);
-}
-
-template<class TInputImage, class TFeatureImage>
-void
-LabelStatisticsOpeningImageFilter<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
-LabelStatisticsOpeningImageFilter<TInputImage, TFeatureImage>
-::EnlargeOutputRequestedRegion(DataObject *)
-{
- this->GetOutput()
- ->SetRequestedRegion( this->GetOutput()->GetLargestPossibleRegion() );
-}
-
-
-template<class TInputImage, class TFeatureImage>
-void
-LabelStatisticsOpeningImageFilter<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->SetBackgroundValue( m_BackgroundValue );
- labelizer->SetNumberOfThreads( this->GetNumberOfThreads() );
- progress->RegisterInternalFilter(labelizer, .3f);
-
- typename LabelObjectValuatorType::Pointer valuator = LabelObjectValuatorType::New();
- valuator->SetInput( labelizer->GetOutput() );
- valuator->SetFeatureImage( this->GetFeatureImage() );
- valuator->SetLabelImage( this->GetInput() );
- 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->SetNumberOfThreads( this->GetNumberOfThreads() );
- progress->RegisterInternalFilter(binarizer, .2f);
-
- binarizer->GraftOutput( this->GetOutput() );
- binarizer->Update();
- this->GraftOutput( binarizer->GetOutput() );
-}
-
-
-template<class TInputImage, class TFeatureImage>
-void
-LabelStatisticsOpeningImageFilter<TInputImage, TFeatureImage>
-::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;
- os << indent << "Attribute: " << LabelObjectType::GetNameFromAttribute(m_Attribute) << " (" << m_Attribute << ")" << std::endl;
-}
-
-}// end namespace itk
-#endif
diff --git a/Utilities/InsightJournal/itkPadLabelMapFilter.h b/Utilities/InsightJournal/itkPadLabelMapFilter.h
deleted file mode 100644
index 01b734171b8a8412d0f7c00c5a65d7a9097ed855..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkPadLabelMapFilter.h
+++ /dev/null
@@ -1,128 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkPadLabelMapFilter.h,v $
- Language: C++
- Date: $Date: 2004/07/11 14:56:38 $
- 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.
-
- Portions of this code are covered under the VTK copyright.
- See VTKCopyright.txt or http://www.kitware.com/VTKCopyright.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 __itkPadLabelMapFilter_h
-#define __itkPadLabelMapFilter_h
-
-#include "itkChangeRegionLabelMapFilter.h"
-
-namespace itk
-{
-
-/** \class PadLabelMapFilter
- * \brief Pad a LabelMap image
- *
- * Pad a label map.
- *
- * The SetPadSize() method can be used to set the pad size of the lower and
- * the upper boundaries in a single call.
- * By default, the filter doesn't pad anything.
- *
- * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
- *
- * \sa CropLabelMapFilter
- * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
- */
-template <class TInputImage>
-class ITK_EXPORT PadLabelMapFilter : public ChangeRegionLabelMapFilter<TInputImage>
-{
-public:
- /** Standard class typedefs. */
- typedef PadLabelMapFilter Self;
- typedef ChangeRegionLabelMapFilter<TInputImage> Superclass;
- typedef SmartPointer<Self> Pointer;
- typedef SmartPointer<const Self> ConstPointer;
-
-
- /** Run-time type information (and related methods). */
- itkTypeMacro(PadLabelMapFilter, ChangeRegionImageFilter);
-
- /** Standard New method. */
- itkNewMacro(Self);
-
- /** Superclass typedefs. */
- typedef typename Superclass::OutputImageType OutputImageType;
- typedef typename Superclass::OutputImagePointer OutputImagePointer;
- typedef typename Superclass::OutputImageRegionType OutputImageRegionType;
- typedef typename Superclass::OutputImagePixelType OutputImagePixelType;
-
- /** 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 InputImageType::PixelType PixelType;
- typedef typename InputImageType::IndexType IndexType;
- typedef typename InputImageType::SizeType SizeType;
- typedef typename InputImageType::RegionType RegionType;
-
- typedef TInputImage TOutputImage;
-
- /** ImageDimension constants */
- itkStaticConstMacro(InputImageDimension, unsigned int,
- TInputImage::ImageDimension);
- itkStaticConstMacro(OutputImageDimension, unsigned int,
- TOutputImage::ImageDimension);
- itkStaticConstMacro(ImageDimension, unsigned int,
- TOutputImage::ImageDimension);
-
- /** Set/Get the cropping sizes for the upper and lower boundaries. */
- itkSetMacro(UpperBoundaryPadSize, SizeType);
- itkGetMacro(UpperBoundaryPadSize, SizeType);
- itkSetMacro(LowerBoundaryPadSize, SizeType);
- itkGetMacro(LowerBoundaryPadSize, SizeType);
-
- void SetPadSize( const SizeType & size )
- {
- this->SetUpperBoundaryPadSize( size );
- this->SetLowerBoundaryPadSize( size );
- }
-
-
- protected:
- PadLabelMapFilter()
- {
- m_UpperBoundaryPadSize.Fill(0);
- m_LowerBoundaryPadSize.Fill(0);
- };
- ~PadLabelMapFilter() {};
-
- virtual void GenerateOutputInformation();
-
- void PrintSelf(std::ostream& os, Indent indent) const;
-
-
-private:
- PadLabelMapFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
- SizeType m_UpperBoundaryPadSize;
- SizeType m_LowerBoundaryPadSize;
-};
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkPadLabelMapFilter.txx"
-#endif
-
-#endif
diff --git a/Utilities/InsightJournal/itkPadLabelMapFilter.txx b/Utilities/InsightJournal/itkPadLabelMapFilter.txx
deleted file mode 100644
index 7a18554bbbf09198c9358bc66983eaf28113859b..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkPadLabelMapFilter.txx
+++ /dev/null
@@ -1,79 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkPadLabelMapFilter.txx,v $
- Language: C++
- Date: $Date: 2004/07/11 14:56:39 $
- 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.
-
- Portions of this code are covered under the VTK copyright.
- See VTKCopyright.txt or http://www.kitware.com/VTKCopyright.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 _itkPadLabelMapFilter_txx
-#define _itkPadLabelMapFilter_txx
-#include "itkPadLabelMapFilter.h"
-
-
-namespace itk
-{
-
-
-template <class TInputImage>
-void
-PadLabelMapFilter<TInputImage>
-::GenerateOutputInformation()
-{
- const TInputImage * inputPtr = this->GetInput();
- if( !inputPtr )
- {
- return;
- }
-
- // Compute the new region size.
- RegionType croppedRegion;
- SizeType sz;
- IndexType idx;
-
- SizeType input_sz =
- inputPtr->GetLargestPossibleRegion().GetSize();
- IndexType input_idx =
- inputPtr->GetLargestPossibleRegion().GetIndex();
-
- idx = input_idx - m_LowerBoundaryPadSize;
- sz = input_sz + (m_UpperBoundaryPadSize + m_LowerBoundaryPadSize);
-
- croppedRegion.SetSize(sz);
- croppedRegion.SetIndex(idx);
-
- // Set extraction region in the superclass.
- this->SetRegion(croppedRegion);
-
- //
- Superclass::GenerateOutputInformation();
-}
-
-
-template <class TInputImage>
-void
-PadLabelMapFilter<TInputImage>
-::PrintSelf(std::ostream& os, Indent indent) const
-{
- Superclass::PrintSelf(os,indent);
-
- os << indent << "UpperBoundaryPadSize: " << m_UpperBoundaryPadSize <<
- std::endl;
- os << indent << "LowerBoundaryPadSize: " << m_LowerBoundaryPadSize <<
- std::endl;
-}
-
-} // end namespace itk
-
-#endif
diff --git a/Utilities/InsightJournal/itkRegionFromReferenceLabelMapFilter.h b/Utilities/InsightJournal/itkRegionFromReferenceLabelMapFilter.h
deleted file mode 100644
index 3185af5934464a41d074a55825e9612a112e8612..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkRegionFromReferenceLabelMapFilter.h
+++ /dev/null
@@ -1,136 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkRegionFromReferenceLabelMapFilter.h,v $
- Language: C++
- Date: $Date: 2004/07/11 14:56:38 $
- 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.
-
- Portions of this code are covered under the VTK copyright.
- See VTKCopyright.txt or http://www.kitware.com/VTKCopyright.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 __itkRegionFromReferenceLabelMapFilter_h
-#define __itkRegionFromReferenceLabelMapFilter_h
-
-#include "itkChangeRegionLabelMapFilter.h"
-
-namespace itk
-{
-
-/** \class RegionFromReferenceLabelMapFilter
- * \brief Set the region from a reference image
- *
- * Change the region of a label map to be the same than the one of a reference image.
- * This filter implement the same feature than its superclass, but with the input region
- * well integrated in the pipeline architecture.
- * If the output can't contain some lines of the objects, they are truncated, or remove.
- * All the objects fully outside the output region are removed.
- *
- * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
- *
- * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
- */
-template <class TInputImage>
-class ITK_EXPORT RegionFromReferenceLabelMapFilter : public ChangeRegionLabelMapFilter<TInputImage>
-{
-public:
- /** Standard class typedefs. */
- typedef RegionFromReferenceLabelMapFilter Self;
- typedef ChangeRegionLabelMapFilter<TInputImage> Superclass;
- typedef SmartPointer<Self> Pointer;
- typedef SmartPointer<const Self> ConstPointer;
-
-
- /** Run-time type information (and related methods). */
- itkTypeMacro(RegionFromReferenceLabelMapFilter, ChangeRegionImageFilter);
-
- /** Standard New method. */
- itkNewMacro(Self);
-
- /** Superclass typedefs. */
- typedef typename Superclass::OutputImageType OutputImageType;
- typedef typename Superclass::OutputImagePointer OutputImagePointer;
- typedef typename Superclass::OutputImageRegionType OutputImageRegionType;
- typedef typename Superclass::OutputImagePixelType OutputImagePixelType;
-
- /** 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 InputImageType::PixelType PixelType;
- typedef typename InputImageType::IndexType IndexType;
- typedef typename InputImageType::SizeType SizeType;
- typedef typename InputImageType::RegionType RegionType;
-
- typedef TInputImage TOutputImage;
-
- /** ImageDimension constants */
- itkStaticConstMacro(InputImageDimension, unsigned int,
- TInputImage::ImageDimension);
- itkStaticConstMacro(OutputImageDimension, unsigned int,
- TOutputImage::ImageDimension);
- itkStaticConstMacro(ImageDimension, unsigned int,
- TOutputImage::ImageDimension);
-
- typedef ImageBase< ImageDimension > ReferenceImageType;
-
- /** Copy the output information from another Image. */
- void SetReferenceImage ( const ReferenceImageType *image )
- {
- itkDebugMacro("setting input ReferenceImage to " << image);
- if( image != static_cast<const ReferenceImageType *>(this->GetInput( 1 )) )
- {
- this->ProcessObject::SetNthInput(1, const_cast< ReferenceImageType *>( image ) );
- this->Modified();
- }
- }
- const ReferenceImageType * GetReferenceImage() const;
-
- /** Set the input image */
- void SetInput1(const TInputImage *input)
- {
- this->SetInput( input );
- }
-
- /** Set the reference image */
- void SetInput2(const ReferenceImageType *input)
- {
- this->SetReferenceImage( input );
- }
-
-
-
- protected:
- RegionFromReferenceLabelMapFilter()
- {
- this->SetNumberOfRequiredInputs(2);
- };
- ~RegionFromReferenceLabelMapFilter() {};
-
- virtual void GenerateOutputInformation();
-
-private:
- RegionFromReferenceLabelMapFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
-};
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkRegionFromReferenceLabelMapFilter.txx"
-#endif
-
-#endif
diff --git a/Utilities/InsightJournal/itkRegionFromReferenceLabelMapFilter.txx b/Utilities/InsightJournal/itkRegionFromReferenceLabelMapFilter.txx
deleted file mode 100644
index 687e4988f166af8244da54f3f32d63576c3c992c..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkRegionFromReferenceLabelMapFilter.txx
+++ /dev/null
@@ -1,54 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkRegionFromReferenceLabelMapFilter.txx,v $
- Language: C++
- Date: $Date: 2004/07/11 14:56:39 $
- 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.
-
- Portions of this code are covered under the VTK copyright.
- See VTKCopyright.txt or http://www.kitware.com/VTKCopyright.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 _itkRegionFromReferenceLabelMapFilter_txx
-#define _itkRegionFromReferenceLabelMapFilter_txx
-#include "itkRegionFromReferenceLabelMapFilter.h"
-
-
-namespace itk
-{
-
-
-template <class TInputImage>
-void
-RegionFromReferenceLabelMapFilter<TInputImage>
-::GenerateOutputInformation()
-{
- Superclass::GenerateOutputInformation();
- this->SetRegion( this->GetReferenceImage()->GetLargestPossibleRegion() );
- this->GetOutput()->SetLargestPossibleRegion( this->GetRegion() );
-}
-
-
-template <class TInputImage>
-const typename RegionFromReferenceLabelMapFilter<TInputImage>::ReferenceImageType *
-RegionFromReferenceLabelMapFilter<TInputImage>
-::GetReferenceImage() const
-{
- Self * surrogate = const_cast< Self * >( this );
- const ReferenceImageType * referenceImage =
- static_cast<const ReferenceImageType *>(surrogate->ProcessObject::GetInput(1));
- return referenceImage;
-}
-
-
-} // end namespace itk
-
-#endif
diff --git a/Utilities/InsightJournal/itkShapeKeepNObjectsLabelMapFilter.h b/Utilities/InsightJournal/itkShapeKeepNObjectsLabelMapFilter.h
deleted file mode 100644
index 14ce3d8eb91ed86c6fa56e2f4d93a1873ea4793c..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkShapeKeepNObjectsLabelMapFilter.h
+++ /dev/null
@@ -1,134 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkShapeKeepNObjectsLabelMapFilter.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 __itkShapeKeepNObjectsLabelMapFilter_h
-#define __itkShapeKeepNObjectsLabelMapFilter_h
-
-#include "itkInPlaceLabelMapFilter.h"
-
-namespace itk {
-/** \class ShapeKeepNObjectsLabelMapFilter
- * \brief keep N objects according to their shape attributes
- *
- * ShapeKeepNObjectsLabelMapFilter keep the N objects in a label collection 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, BinaryShapeKeepNObjectsImageFilter, LabelStatisticsKeepNObjectsImageFilter
- * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
- */
-template<class TImage>
-class ITK_EXPORT ShapeKeepNObjectsLabelMapFilter :
- public InPlaceLabelMapFilter<TImage>
-{
-public:
- /** Standard class typedefs. */
- typedef ShapeKeepNObjectsLabelMapFilter 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 typename LabelObjectType::AttributeType AttributeType;
-
- /** ImageDimension constants */
- itkStaticConstMacro(ImageDimension, unsigned int,
- TImage::ImageDimension);
-
- /** Standard New method. */
- itkNewMacro(Self);
-
- /** Runtime information support. */
- itkTypeMacro(ShapeKeepNObjectsLabelMapFilter,
- 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 );
-
- /**
- * 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:
- ShapeKeepNObjectsLabelMapFilter();
- ~ShapeKeepNObjectsLabelMapFilter() {};
-
- void GenerateData();
-
- template <class TAttributeAccessor> void TemplatedGenerateData();
-
- void PrintSelf(std::ostream& os, Indent indent) const;
-
- bool m_ReverseOrdering;
- unsigned long m_NumberOfObjects;
- AttributeType m_Attribute;
-
-private:
- ShapeKeepNObjectsLabelMapFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
-} ; // end of class
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkShapeKeepNObjectsLabelMapFilter.txx"
-#endif
-
-#endif
-
-
diff --git a/Utilities/InsightJournal/itkShapeKeepNObjectsLabelMapFilter.txx b/Utilities/InsightJournal/itkShapeKeepNObjectsLabelMapFilter.txx
deleted file mode 100644
index b6216bb6071b09d7845b085d5b59bec726208690..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkShapeKeepNObjectsLabelMapFilter.txx
+++ /dev/null
@@ -1,150 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkShapeKeepNObjectsLabelMapFilter.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 __itkShapeKeepNObjectsLabelMapFilter_txx
-#define __itkShapeKeepNObjectsLabelMapFilter_txx
-
-#include "itkShapeKeepNObjectsLabelMapFilter.h"
-#include "itkProgressReporter.h"
-#include "itkLabelObjectUtils.h"
-
-
-namespace itk {
-
-template <class TImage>
-ShapeKeepNObjectsLabelMapFilter<TImage>
-::ShapeKeepNObjectsLabelMapFilter()
-{
- m_ReverseOrdering = false;
- m_NumberOfObjects = 1;
- m_Attribute = LabelObjectType::SIZE;
-}
-
-
-template <class TImage>
-void
-ShapeKeepNObjectsLabelMapFilter<TImage>
-::GenerateData()
-{
- switch( m_Attribute )
- {
- case LabelObjectType::SIZE:
- TemplatedGenerateData< typename Functor::SizeLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::PHYSICAL_SIZE:
- TemplatedGenerateData< typename Functor::PhysicalSizeLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::SIZE_REGION_RATIO:
- TemplatedGenerateData< typename Functor::SizeRegionRatioLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::REGION_ELONGATION:
- TemplatedGenerateData< typename Functor::RegionElongationLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::SIZE_ON_BORDER:
- TemplatedGenerateData< typename Functor::SizeOnBorderLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::PHYSICAL_SIZE_ON_BORDER:
- TemplatedGenerateData< typename Functor::PhysicalSizeOnBorderLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::FERET_DIAMETER:
- TemplatedGenerateData< typename Functor::FeretDiameterLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::BINARY_ELONGATION:
- TemplatedGenerateData< typename Functor::BinaryElongationLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::PERIMETER:
- TemplatedGenerateData< typename Functor::PerimeterLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::ROUNDNESS:
- TemplatedGenerateData< typename Functor::RoundnessLabelObjectAccessor< LabelObjectType > >();
- break;
- default:
- itkExceptionMacro(<< "Unknown attribute type");
- break;
- }
-}
-
-
-template <class TImage>
-template <class TAttributeAccessor>
-void
-ShapeKeepNObjectsLabelMapFilter<TImage>
-::TemplatedGenerateData()
-{
- // 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 )
- {
- Functor::LabelObjectReverseComparator< LabelObjectType, TAttributeAccessor > comparator;
- std::nth_element( labelObjects.begin(), end, labelObjects.end(), comparator );
- }
- else
- {
- Functor::LabelObjectComparator< LabelObjectType, TAttributeAccessor > 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>
-void
-ShapeKeepNObjectsLabelMapFilter<TImage>
-::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;
- os << indent << "Attribute: " << LabelObjectType::GetNameFromAttribute(m_Attribute) << " (" << m_Attribute << ")" << std::endl;
-}
-
-}// end namespace itk
-#endif
diff --git a/Utilities/InsightJournal/itkShapeLabelMapFilter.h b/Utilities/InsightJournal/itkShapeLabelMapFilter.h
deleted file mode 100644
index cc8aa86d41a7380b87771f61e67ca325eb24ba85..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkShapeLabelMapFilter.h
+++ /dev/null
@@ -1,172 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkShapeLabelMapFilter.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 __itkShapeLabelMapFilter_h
-#define __itkShapeLabelMapFilter_h
-#include "itkLabelPerimeterEstimationCalculator.h"
-
-#include "itkInPlaceLabelMapFilter.h"
-
-#define PI 3.14159265358979323846
-
-namespace itk {
-/** \class ShapeLabelMapFilter
- * \brief The valuator class for the ShapeLabelObject
- *
- * ShapeLabelMapFilter can be used to set the attributes values
- * of the ShapeLabelObject in a LabelMap.
- *
- * ShapeLabelMapFilter take an optional parameter, used only to optimize
- * the computation time and the memory usage when the perimeter or the feret diameter
- * are used: the exact copy of the input LabelMap but stored in an Image.
- * It can be set with SetLabelImage(). It is cleared at the end of the computation, and
- * so must be reset before running Update() again. It is not part of the pipeline management
- * design, to let the subclasses of ShapeLabelMapFilter use the
- * pipeline desing to specify a really required input.
- *
- * \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 TLabelImage=Image< typename TImage::PixelType, TImage::ImageDimension > >
-class ITK_EXPORT ShapeLabelMapFilter :
- public InPlaceLabelMapFilter<TImage>
-{
-public:
- /** Standard class typedefs. */
- typedef ShapeLabelMapFilter 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::SizeType SizeType;
- typedef typename ImageType::LabelObjectType LabelObjectType;
- typedef typename LabelObjectType::MatrixType MatrixType;
- typedef typename LabelObjectType::VectorType VectorType;
-
- typedef TLabelImage LabelImageType;
- typedef typename LabelImageType::Pointer LabelImagePointer;
- typedef typename LabelImageType::ConstPointer LabelImageConstPointer;
- typedef typename LabelImageType::PixelType LabelPixelType;
-
- /** ImageDimension constants */
- itkStaticConstMacro(ImageDimension, unsigned int,
- TImage::ImageDimension);
-
- typedef LabelPerimeterEstimationCalculator< LabelImageType > PerimeterCalculatorType;
-
- /** Standard New method. */
- itkNewMacro(Self);
-
- /** Runtime information support. */
- itkTypeMacro(ShapeLabelMapFilter,
- 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 whether the maximum Feret diameter should be computed or not. The
- * defaut value is false, because of the high computation time required.
- */
- itkSetMacro(ComputeFeretDiameter, bool);
- itkGetConstReferenceMacro(ComputeFeretDiameter, bool);
- itkBooleanMacro(ComputeFeretDiameter);
-
- /**
- * Set/Get whether the perimeter should be computed or not. The defaut value
- * is false, because of the high computation time required.
- */
- itkSetMacro(ComputePerimeter, bool);
- itkGetConstReferenceMacro(ComputePerimeter, bool);
- itkBooleanMacro(ComputePerimeter);
-
-
- /** Set the label image */
- void SetLabelImage( const TLabelImage *input )
- {
- m_LabelImage = input;
- }
-
- /** */
- static long factorial( long n );
-
- /** */
- static long doubleFactorial( long n );
-
- /** */
- static double gammaN2p1( long n );
-
- /** */
- static double hyperSphereVolume( double radius );
-
- /** */
- static double hyperSpherePerimeter( double radius );
-
- /** */
- static double hyperSphereRadiusFromVolume( double volume );
-
-
-protected:
- ShapeLabelMapFilter();
- ~ShapeLabelMapFilter() {};
-
- virtual void ThreadedGenerateData( LabelObjectType * labelObject );
-
- virtual void BeforeThreadedGenerateData();
-
- virtual void AfterThreadedGenerateData();
-
- void PrintSelf(std::ostream& os, Indent indent) const;
-
-private:
- ShapeLabelMapFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
- bool m_ComputeFeretDiameter;
-
- bool m_ComputePerimeter;
-
- LabelImageConstPointer m_LabelImage;
-
- typename PerimeterCalculatorType::Pointer m_PerimeterCalculator;
-
-} ; // end of class
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkShapeLabelMapFilter.txx"
-#endif
-
-#endif
-
-
diff --git a/Utilities/InsightJournal/itkShapeLabelMapFilter.txx b/Utilities/InsightJournal/itkShapeLabelMapFilter.txx
deleted file mode 100644
index 27b3e54bea4d32643602dfcd7a0103bc0f3350a4..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkShapeLabelMapFilter.txx
+++ /dev/null
@@ -1,566 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkShapeLabelMapFilter.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 __itkShapeLabelMapFilter_txx
-#define __itkShapeLabelMapFilter_txx
-
-#include "itkShapeLabelMapFilter.h"
-#include "itkProgressReporter.h"
-#include "itkNeighborhoodIterator.h"
-#include "itkLabelMapToLabelImageFilter.h"
-#include "itkConstantBoundaryCondition.h"
-#include "vnl/algo/vnl_real_eigensystem.h"
-#include "vnl/algo/vnl_symmetric_eigensystem.h"
-
-
-namespace itk {
-
-template <class TImage, class TLabelImage>
-ShapeLabelMapFilter<TImage, TLabelImage>
-::ShapeLabelMapFilter()
-{
- m_ComputeFeretDiameter = false;
- m_ComputePerimeter = false;
-}
-
-
-template<class TImage, class TLabelImage>
-void
-ShapeLabelMapFilter<TImage, TLabelImage>
-::BeforeThreadedGenerateData()
-{
- Superclass::BeforeThreadedGenerateData();
-
- // generate the label image, if needed
- if( m_ComputeFeretDiameter || m_ComputePerimeter )
- {
- if( !m_LabelImage )
- {
- // generate an image of the labelized image
- typedef LabelMapToLabelImageFilter< TImage, LabelImageType > LCI2IType;
- typename LCI2IType::Pointer lci2i = LCI2IType::New();
- lci2i->SetInput( this->GetOutput() );
- // respect the number of threads of the filter
- lci2i->SetNumberOfThreads( this->GetNumberOfThreads() );
- lci2i->Update();
- m_LabelImage = lci2i->GetOutput();
- }
- }
-
- // delegate the computation of the perimeter to a dedicated calculator
- if( m_ComputePerimeter )
- {
- m_PerimeterCalculator = PerimeterCalculatorType::New();
- m_PerimeterCalculator->SetImage( m_LabelImage );
-// m_PerimeterCalculator->SetNumberOfThreads( this->GetNumberOfThreads() );
- m_PerimeterCalculator->Compute();
- }
-
-}
-
-
-template<class TImage, class TLabelImage>
-void
-ShapeLabelMapFilter<TImage, TLabelImage>
-::ThreadedGenerateData( LabelObjectType * labelObject )
-{
- ImageType * output = this->GetOutput();
- const LabelPixelType & label = labelObject->GetLabel();
-
- // TODO: compute sizePerPixel, borderMin and borderMax in BeforeThreadedGenerateData() ?
-
- // compute the size per pixel, to be used later
- double sizePerPixel = 1;
- for( int i=0; i<ImageDimension; i++ )
- {
- sizePerPixel *= output->GetSpacing()[i];
- }
-
- typename std::vector< double > sizePerPixelPerDimension;
- for( int i=0; i<ImageDimension; i++ )
- {
- sizePerPixelPerDimension.push_back( sizePerPixel / output->GetSpacing()[i] );
- }
-
- // compute the max the index on the border of the image
- IndexType borderMin = output->GetLargestPossibleRegion().GetIndex();
- IndexType borderMax = borderMin;
- for( int i=0; i<ImageDimension; i++ )
- {
- borderMax[i] += borderMin[i] + output->GetLargestPossibleRegion().GetSize()[i] - 1;
- }
-
- // init the vars
- unsigned long size = 0;
- ContinuousIndex< double, ImageDimension> centroid;
- centroid.Fill( 0 );
- IndexType mins;
- mins.Fill( NumericTraits< long >::max() );
- IndexType maxs;
- maxs.Fill( NumericTraits< long >::NonpositiveMin() );
- unsigned long sizeOnBorder = 0;
- double physicalSizeOnBorder = 0;
- MatrixType centralMoments;
- centralMoments.Fill( 0 );
-
- typename LabelObjectType::LineContainerType::const_iterator lit;
- typename LabelObjectType::LineContainerType & lineContainer = labelObject->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 size
- size += length;
-
- // update the centroid - and report the progress
- // first, update the axes which are not 0
- for( int i=1; i<ImageDimension; i++ )
- {
- centroid[i] += length * idx[i];
- }
- // then, update the axis 0
- centroid[0] += idx[0] * length + ( length * ( length - 1 ) ) / 2.0;
-
- // 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;
- }
-
- // object is on a border ?
- bool isOnBorder = false;
- for( int i=1; i<ImageDimension; i++)
- {
- if( idx[i] == borderMin[i] || idx[i] == borderMax[i])
- {
- isOnBorder = true;
- break;
- }
- }
- if( isOnBorder )
- {
- // the line touch a border on a dimension other than 0, so
- // all the line touch a border
- sizeOnBorder += length;
- }
- else
- {
- // we must check for the dimension 0
- bool isOnBorder0 = false;
- if( idx[0] == borderMin[0] )
- {
- // one more pixel on the border
- sizeOnBorder++;
- isOnBorder0 = true;
- }
- if( !isOnBorder0 || length > 1 )
- {
- // we can check for the end of the line
- if( idx[0] + (long)length - 1 == borderMax[0] )
- {
- // one more pixel on the border
- sizeOnBorder++;
- }
- }
- }
-
- // physical size on border
- // first, the dimension 0
- if( idx[0] == borderMin[0] )
- {
- // the begining of the line
- physicalSizeOnBorder += sizePerPixelPerDimension[0];
- }
- if( idx[0] + (long)length - 1 == borderMax[0] )
- {
- // and the end of the line
- physicalSizeOnBorder += sizePerPixelPerDimension[0];
- }
- // then the other dimensions
- for( int i=1; i<ImageDimension; i++ )
- {
- if( idx[i] == borderMin[i] )
- {
- // one border
- physicalSizeOnBorder += sizePerPixelPerDimension[i] * length;
- }
- if( idx[i] == borderMax[i] )
- {
- // and the other
- physicalSizeOnBorder += sizePerPixelPerDimension[i] * length;
- }
- }
-
- // moments computation
-// ****************************************************************
-// that commented code is the basic implementation. The next peace of code
-// give the same result in a much efficient way, by using expended formulae
-// allowed by the binary case instead of loops.
-// ****************************************************************
-// long endIdx0 = idx[0] + length;
-// for( IndexType iidx = idx; iidx[0]<endIdx0; iidx[0]++)
-// {
-// typename LabelObjectType::CentroidType pP;
-// output->TransformIndexToPhysicalPoint(iidx, pP);
-//
-// for(unsigned int i=0; i<ImageDimension; i++)
-// {
-// for(unsigned int j=0; j<ImageDimension; j++)
-// {
-// centralMoments[i][j] += pP[i] * pP[j];
-// }
-// }
-// }
- // get the physical position and the spacing - they are used several times later
- typename LabelObjectType::CentroidType physicalPosition;
- output->TransformIndexToPhysicalPoint( idx, physicalPosition );
- const typename ImageType::SpacingType & spacing = output->GetSpacing();
- // the sum of x positions, also reused several times
- double sumX = length * ( physicalPosition[0] + ( spacing[0] * ( length - 1 ) ) / 2.0 );
- // the real job - the sum of square of x positions
- // that's the central moments for dims 0, 0
- centralMoments[0][0] += length * ( physicalPosition[0] * physicalPosition[0]
- + spacing[0] * ( length - 1 ) * ( ( spacing[0] * ( 2 * length - 1 ) ) / 6.0 + physicalPosition[0] ) );
- // the other ones
- for( int i=1; i<ImageDimension; i++ )
- {
- // do this one here to avoid the double assigment in the following loop
- // when i == j
- centralMoments[i][i] += length * physicalPosition[i] * physicalPosition[i];
- // central moments are symetrics, so avoid to compute them 2 times
- for( int j=i+1; j<ImageDimension; j++ )
- {
- // note that we won't use that code if the image dimension is less than 3
- // --> the tests should be in 3D at least
- double cm = length * physicalPosition[i] * physicalPosition[j];
- centralMoments[i][j] += cm;
- centralMoments[j][i] += cm;
- }
- // the last moments: the ones for the dimension 0
- double cm = sumX * physicalPosition[i];
- centralMoments[i][0] += cm;
- centralMoments[0][i] += cm;
- }
-
- }
-
- // final computation
- typename LabelObjectType::RegionType::SizeType regionSize;
- double minSize = NumericTraits< double >::max();
- double maxSize = NumericTraits< double >::NonpositiveMin();
- for( int i=0; i<ImageDimension; i++ )
- {
- centroid[i] /= size;
- regionSize[i] = maxs[i] - mins[i] + 1;
- double s = regionSize[i] * output->GetSpacing()[i];
- minSize = std::min( s, minSize );
- maxSize = std::max( s, maxSize );
- for(unsigned int j=0; j<ImageDimension; j++)
- {
- centralMoments[i][j] /= size;
- }
- }
- typename LabelObjectType::RegionType region( mins, regionSize );
- typename LabelObjectType::CentroidType physicalCentroid;
- output->TransformContinuousIndexToPhysicalPoint( centroid, physicalCentroid );
-
- // Center the second order moments
- for(unsigned int i=0; i<ImageDimension; i++)
- {
- for(unsigned int j=0; j<ImageDimension; j++)
- {
- centralMoments[i][j] -= physicalCentroid[i] * physicalCentroid[j];
- }
- }
-
- // Compute principal moments and axes
- VectorType principalMoments;
- vnl_symmetric_eigensystem<double> eigen( centralMoments.GetVnlMatrix() );
- vnl_diag_matrix<double> pm = eigen.D;
- for(unsigned int i=0; i<ImageDimension; i++)
- {
-// principalMoments[i] = 4 * vcl_sqrt( pm(i,i) );
- principalMoments[i] = pm(i,i);
- }
- MatrixType principalAxes = eigen.V.transpose();
-
- // Add a final reflection if needed for a proper rotation,
- // by multiplying the last row by the determinant
- vnl_real_eigensystem eigenrot( principalAxes.GetVnlMatrix() );
- vnl_diag_matrix< vcl_complex<double> > eigenval = eigenrot.D;
- vcl_complex<double> det( 1.0, 0.0 );
-
- for(unsigned int i=0; i<ImageDimension; i++)
- {
- det *= eigenval( i, i );
- }
-
- for(unsigned int i=0; i<ImageDimension; i++)
- {
- principalAxes[ ImageDimension-1 ][i] *= std::real( det );
- }
-
- double elongation = 0;
- if( principalMoments[0] != 0 )
- {
-// elongation = principalMoments[ImageDimension-1] / principalMoments[0];
- elongation = vcl_sqrt(principalMoments[ImageDimension-1] / principalMoments[0]);
- }
-
- double physicalSize = size * sizePerPixel;
- double equivalentRadius = hyperSphereRadiusFromVolume( physicalSize );
- double equivalentPerimeter = hyperSpherePerimeter( equivalentRadius );
-
- // compute equilalent ellipsoid radius
- VectorType ellipsoidSize;
- double edet = 1.0;
- for(unsigned int i=0; i<ImageDimension; i++)
- {
- edet *= principalMoments[i];
- }
- edet = vcl_pow( edet, 1.0/ImageDimension );
- for(unsigned int i=0; i<ImageDimension; i++)
- {
- ellipsoidSize[i] = 2.0 * equivalentRadius * vcl_sqrt( principalMoments[i] / edet );
- }
-
- // set the values in the object
- labelObject->SetSize( size );
- labelObject->SetPhysicalSize( physicalSize );
- labelObject->SetRegion( region );
- labelObject->SetCentroid( physicalCentroid );
- labelObject->SetRegionElongation( maxSize / minSize );
- labelObject->SetSizeRegionRatio( size / (double)region.GetNumberOfPixels() );
- labelObject->SetSizeOnBorder( sizeOnBorder );
- labelObject->SetPhysicalSizeOnBorder( physicalSizeOnBorder );
- labelObject->SetBinaryPrincipalMoments( principalMoments );
- labelObject->SetBinaryPrincipalAxes( principalAxes );
- labelObject->SetBinaryElongation( elongation );
- labelObject->SetEquivalentRadius( equivalentRadius );
- labelObject->SetEquivalentPerimeter( equivalentPerimeter );
- labelObject->SetEquivalentEllipsoidSize( ellipsoidSize );
-
- if( m_ComputeFeretDiameter )
- {
- const PixelType & label = labelObject->GetLabel();
-
- // init the vars
- unsigned long size = 0;
- typedef typename std::deque< IndexType > IndexListType;
- IndexListType idxList;
-
- // the iterators
- typename LabelObjectType::LineContainerType::const_iterator lit;
- typename LabelObjectType::LineContainerType & lineContainer = labelObject->GetLineContainer();
-
- typedef typename itk::ConstNeighborhoodIterator< LabelImageType > NeighborIteratorType;
- SizeType neighborHoodRadius;
- neighborHoodRadius.Fill( 1 );
- NeighborIteratorType it( neighborHoodRadius, m_LabelImage, m_LabelImage->GetBufferedRegion() );
- ConstantBoundaryCondition<LabelImageType> lcbc;
- // use label + 1 to have a label different of the current label on the border
- lcbc.SetConstant( label + 1 );
- it.OverrideBoundaryCondition( &lcbc );
- it.GoToBegin();
-
- // iterate over all the lines
- 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]++)
- {
-
- // move the iterator to the new location
- it += idx - it.GetIndex();
-
- // push the pixel in the list if it is on the border of the object
- for (unsigned i = 0; i < it.Size(); i++)
- {
- if( it.GetPixel(i) != label )
- {
- idxList.push_back( idx );
- size++;
- break;
- }
- }
- }
- }
-
- // we can now search the feret diameter
- double feretDiameter = 0;
- for( typename IndexListType::const_iterator iIt1 = idxList.begin();
- iIt1 != idxList.end();
- iIt1++ )
- {
- typename IndexListType::const_iterator iIt2 = iIt1;
- for( iIt2++; iIt2 != idxList.end(); iIt2++ )
- {
- // Compute the length between the 2 indexes
- double length = 0;
- for( int i=0; i<ImageDimension; i++ )
- {
- length += vcl_pow( ( iIt1->operator[]( i ) - iIt2->operator[]( i ) ) * output->GetSpacing()[i], 2 );
- }
- if( feretDiameter < length )
- {
- feretDiameter = length;
- }
- }
- }
- // final computation
- feretDiameter = vcl_sqrt( feretDiameter );
-
- // finally put the values in the label object
- labelObject->SetFeretDiameter( feretDiameter );
-
- }
-
-
- // be sure tha the calculator has the perimeter estimation for that label.
- // The calculator may not have the label if the object is only on a border.
- // It will occurre for sure when processing a 2D image with a 3D filter.
- if( m_ComputePerimeter && m_PerimeterCalculator->HasLabel( label ) )
- {
- double perimeter = m_PerimeterCalculator->GetPerimeter( label );
- labelObject->SetPerimeter( perimeter );
- labelObject->SetRoundness( equivalentPerimeter / perimeter );
- }
-
-// std::cout << std::endl;
-// labelObject->Print( std::cout );
-// std::cout << std::endl;
-
-}
-
-
-template<class TImage, class TLabelImage>
-void
-ShapeLabelMapFilter<TImage, TLabelImage>
-::AfterThreadedGenerateData()
-{
- Superclass::AfterThreadedGenerateData();
-
- // release the label image
- m_LabelImage = NULL;
- // and the perimeter calculator
- m_PerimeterCalculator = NULL;
-}
-
-
-template<class TImage, class TLabelImage>
-void
-ShapeLabelMapFilter<TImage, TLabelImage>
-::PrintSelf(std::ostream& os, Indent indent) const
-{
- Superclass::PrintSelf(os,indent);
-
- os << indent << "ComputeFeretDiameter: " << m_ComputeFeretDiameter << std::endl;
- os << indent << "ComputePerimeter: " << m_ComputePerimeter << std::endl;
-}
-
-
-template<class TImage, class TLabelImage>
-long
-ShapeLabelMapFilter<TImage, TLabelImage>
-::factorial( long n )
-{
- if( n < 1 )
- {
- return 1;
- }
- return n * factorial( n - 1 );
-}
-
-
-template<class TImage, class TLabelImage>
-long
-ShapeLabelMapFilter<TImage, TLabelImage>
-::doubleFactorial( long n )
-{
- if( n < 2 )
- {
- return 1;
- }
- return n * doubleFactorial( n - 2 );
-}
-
-
-template<class TImage, class TLabelImage>
-double
-ShapeLabelMapFilter<TImage, TLabelImage>
-::gammaN2p1( long n )
-{
- bool even = n % 2 == 0;
- if( even )
- {
- return factorial( n / 2 );
- }
- else
- {
- return vcl_sqrt( PI ) * doubleFactorial( n ) / vcl_pow( 2, ( n + 1 ) / 2.0 );
- }
-}
-
-
-template<class TImage, class TLabelImage>
-double
-ShapeLabelMapFilter<TImage, TLabelImage>
-::hyperSphereVolume( double radius )
-{
- return vcl_pow( PI, ImageDimension / 2.0 ) * vcl_pow( radius, ImageDimension ) / gammaN2p1( ImageDimension );
-}
-
-
-template<class TImage, class TLabelImage>
-double
-ShapeLabelMapFilter<TImage, TLabelImage>
-::hyperSpherePerimeter( double radius )
-{
- return ImageDimension * hyperSphereVolume( radius ) / radius;
-}
-
-
-template<class TImage, class TLabelImage>
-double
-ShapeLabelMapFilter<TImage, TLabelImage>
-::hyperSphereRadiusFromVolume( double volume )
-{
- return vcl_pow( volume * gammaN2p1( ImageDimension ) / vcl_pow( PI, ImageDimension / 2.0 ), 1.0 / ImageDimension );
-}
-
-
-
-
-}// end namespace itk
-#endif
diff --git a/Utilities/InsightJournal/itkShapeLabelObject.h b/Utilities/InsightJournal/itkShapeLabelObject.h
deleted file mode 100644
index d264f820d98513e151c75a9006ecc2ef2b11e7bf..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkShapeLabelObject.h
+++ /dev/null
@@ -1,801 +0,0 @@
-/*=========================================================================
-
- 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 __itkShapeLabelObject_h
-#define __itkShapeLabelObject_h
-
-#include "itkLabelObject.h"
-#include "itkLabelMap.h"
-#include "itkAffineTransform.h"
-#include "itkMatrix.h"
-
-namespace itk
-{
-
-
-namespace Functor {
-
-template< class TLabelObject >
-class ITK_EXPORT SizeLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef unsigned long AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetSize();
- }
-};
-
-template< class TLabelObject >
-class ITK_EXPORT PhysicalSizeLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef double AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetPhysicalSize();
- }
-};
-
-template< class TLabelObject >
-class ITK_EXPORT RegionElongationLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef double AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetRegionElongation();
- }
-};
-
-template< class TLabelObject >
-class ITK_EXPORT SizeRegionRatioLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef double AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetSizeRegionRatio();
- }
-};
-
-template< class TLabelObject >
-class ITK_EXPORT SizeOnBorderLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef unsigned long AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetSizeOnBorder();
- }
-};
-
-template< class TLabelObject >
-class ITK_EXPORT PhysicalSizeOnBorderLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef double AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetPhysicalSizeOnBorder();
- }
-};
-
-template< class TLabelObject >
-class ITK_EXPORT CentroidLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef typename LabelObjectType::CentroidType AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetCentroid();
- }
-};
-
-template< class TLabelObject >
-class ITK_EXPORT FeretDiameterLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef double AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetFeretDiameter();
- }
-};
-
-template< class TLabelObject >
-class ITK_EXPORT BinaryPrincipalMomentsLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef typename LabelObjectType::VectorType AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetBinaryPrincipalMoments();
- }
-};
-
-template< class TLabelObject >
-class ITK_EXPORT BinaryPrincipalAxesLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef typename LabelObjectType::MatrixType AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetBinaryPrincipalAxes();
- }
-};
-
-template< class TLabelObject >
-class ITK_EXPORT BinaryElongationLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef double AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetBinaryElongation();
- }
-};
-
-template< class TLabelObject >
-class ITK_EXPORT PerimeterLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef double AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetPerimeter();
- }
-};
-
-template< class TLabelObject >
-class ITK_EXPORT RoundnessLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef double AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetRoundness();
- }
-};
-
-template< class TLabelObject >
-class ITK_EXPORT EquivalentRadiusLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef double AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetEquivalentRadius();
- }
-};
-
-template< class TLabelObject >
-class ITK_EXPORT EquivalentPerimeterLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef double AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetEquivalentPerimeter();
- }
-};
-
-template< class TLabelObject >
-class ITK_EXPORT EquivalentEllipsoidSizeLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef typename LabelObjectType::VectorType AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetEquivalentEllipsoidSize();
- }
-};
-
-}
-
-
-/** \class ShapeLabelObject
- * \brief A Label object to store the common attributes related to the shape of the object
- *
- * ShapeLabelObject stores the common attributes related to the shape of the object
- *
- * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
- *
- * \ingroup DataRepresentation
- */
-template < class TLabel, unsigned int VImageDimension >
-class ITK_EXPORT ShapeLabelObject : public LabelObject< TLabel, VImageDimension >
-{
-public:
- /** Standard class typedefs */
- typedef ShapeLabelObject 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(ShapeLabelObject, 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 unsigned int AttributeType;
- static const AttributeType SIZE=0;
- static const AttributeType PHYSICAL_SIZE=1;
- static const AttributeType REGION_ELONGATION=2;
- static const AttributeType SIZE_REGION_RATIO=3;
- static const AttributeType CENTROID=4;
- static const AttributeType REGION=5;
- static const AttributeType SIZE_ON_BORDER=6;
- static const AttributeType PHYSICAL_SIZE_ON_BORDER=7;
- static const AttributeType FERET_DIAMETER=8;
- static const AttributeType BINARY_PRINCIPAL_MOMENTS=9;
- static const AttributeType BINARY_PRINCIPAL_AXES=10;
- static const AttributeType BINARY_ELONGATION=11;
- static const AttributeType PERIMETER=12;
- static const AttributeType ROUNDNESS=13;
- static const AttributeType EQUIVALENT_RADIUS=14;
- static const AttributeType EQUIVALENT_PERIMETER=15;
- static const AttributeType EQUIVALENT_ELLIPSOID_RADIUS=16;
-
- static AttributeType GetAttributeFromName( const std::string & s )
- {
- if( s == "Size" )
- {
- return SIZE;
- }
- else if( s == "PhysicalSize" )
- {
- return PHYSICAL_SIZE;
- }
- else if( s == "RegionElongation" )
- {
- return REGION_ELONGATION;
- }
- else if( s == "SizeRegionRatio" )
- {
- return SIZE_REGION_RATIO;
- }
- else if( s == "Centroid" )
- {
- return CENTROID;
- }
- else if( s == "Region" )
- {
- return REGION;
- }
- else if( s == "SizeOnBorder" )
- {
- return SIZE_ON_BORDER;
- }
- else if( s == "PhysicalSizeOnBorder" )
- {
- return PHYSICAL_SIZE_ON_BORDER;
- }
- else if( s == "FeretDiameter" )
- {
- return FERET_DIAMETER;
- }
- else if( s == "BinaryPrincipalMoments" )
- {
- return BINARY_PRINCIPAL_MOMENTS;
- }
- else if( s == "BinaryPrincipalAxes" )
- {
- return BINARY_PRINCIPAL_AXES;
- }
- else if( s == "BinaryElongation" )
- {
- return BINARY_ELONGATION;
- }
- else if( s == "Perimeter" )
- {
- return PERIMETER;
- }
- else if( s == "Roundness" )
- {
- return ROUNDNESS;
- }
- else if( s == "EquivalentRadius" )
- {
- return EQUIVALENT_RADIUS;
- }
- else if( s == "EquivalentPerimeter" )
- {
- return EQUIVALENT_PERIMETER;
- }
- else if( s == "EquivalentEllipsoidSize" )
- {
- return EQUIVALENT_ELLIPSOID_RADIUS;
- }
- // can't recognize the namespace
- throw std::runtime_error("Unknown attribute.");
- }
-
- static std::string GetNameFromAttribute( const AttributeType & a )
- {
- switch( a )
- {
- case SIZE:
- return "Size";
- break;
- case PHYSICAL_SIZE:
- return "PhysicalSize";
- break;
- case REGION_ELONGATION:
- return "RegionElongation";
- break;
- case SIZE_REGION_RATIO:
- return "SizeRegionRatio";
- break;
- case CENTROID:
- return "Centroid";
- case REGION:
- return "Region";
- break;
- case SIZE_ON_BORDER:
- return "SizeOnBorder";
- break;
- case PHYSICAL_SIZE_ON_BORDER:
- return "PhysicalSizeOnBorder";
- break;
- case FERET_DIAMETER:
- return "FeretDiameter";
- break;
- case BINARY_PRINCIPAL_MOMENTS:
- return "BinaryPrincipalMoments";
- break;
- case BINARY_PRINCIPAL_AXES:
- return "BinaryPrincipalAxes";
- break;
- case BINARY_ELONGATION:
- return "BinaryElongation";
- break;
- case PERIMETER:
- return "Perimeter";
- break;
- case ROUNDNESS:
- return "Roundness";
- break;
- case EQUIVALENT_RADIUS:
- return "EquivalentRadius";
- break;
- case EQUIVALENT_PERIMETER:
- return "EquivalentPerimeter";
- break;
- case EQUIVALENT_ELLIPSOID_RADIUS:
- return "EquivalentEllipsoidSize";
- break;
- }
- // can't recognize the namespace
- throw std::runtime_error("Unknown attribute.");
- }
-
- typedef ImageRegion< ImageDimension > RegionType;
-
- typedef typename itk::Point<double, ImageDimension> CentroidType;
-
- typedef Matrix< double, ImageDimension, ImageDimension > MatrixType;
-
- typedef Vector< double, ImageDimension > VectorType;
-
-/* itkGetConstMacro( Region, RegionType );
- itkSetMacro( Region, RegionType );*/
- const RegionType & GetRegion() const
- {
- return m_Region;
- }
-
- void SetRegion( const RegionType & v )
- {
- m_Region = v;
- }
-
-// itkGetConstMacro( PhysicalSize, double );
-// itkSetMacro( PhysicalSize, double );
- const double & GetPhysicalSize() const
- {
- return m_PhysicalSize;
- }
-
- void SetPhysicalSize( const double & v )
- {
- m_PhysicalSize = v;
- }
-
-// itkGetConstMacro( Size, unsigned long );
-// itkSetMacro( Size, unsigned long );
- const unsigned long & GetSize() const
- {
- return m_Size;
- }
-
- void SetSize( const unsigned long & v )
- {
- m_Size = v;
- }
-
-// itkGetConstMacro( Centroid, CentroidType );
-// itkSetMacro( Centroid, CentroidType );
- const CentroidType & GetCentroid() const
- {
- return m_Centroid;
- }
-
- void SetCentroid( const CentroidType & centroid )
- {
- m_Centroid = centroid;
- }
-
-// itkGetConstMacro( RegionElongation, double );
-// itkSetMacro( RegionElongation, double );
- const double & GetRegionElongation() const
- {
- return m_RegionElongation;
- }
-
- void SetRegionElongation( const double & v )
- {
- m_RegionElongation = v;
- }
-
-// itkGetConstMacro( SizeRegionRatio, double );
-// itkSetMacro( SizeRegionRatio, double );
- const double & GetSizeRegionRatio() const
- {
- return m_SizeRegionRatio;
- }
-
- void SetSizeRegionRatio( const double & v )
- {
- m_SizeRegionRatio = v;
- }
-
-// itkGetConstMacro( SizeOnBorder, bool );
-// itkSetMacro( SizeOnBorder, bool );
- const unsigned long & GetSizeOnBorder() const
- {
- return m_SizeOnBorder;
- }
-
- void SetSizeOnBorder( const unsigned long & v )
- {
- m_SizeOnBorder = v;
- }
-
-// itkGetConstMacro( PhysicalSizeOnBorder, double );
-// itkSetMacro( PhysicalSizeOnBorder, double );
- const double & GetPhysicalSizeOnBorder() const
- {
- return m_PhysicalSizeOnBorder;
- }
-
- void SetPhysicalSizeOnBorder( const double & v )
- {
- m_PhysicalSizeOnBorder = v;
- }
-
-// itkGetConstMacro( FeretDiameter, double );
-// itkSetMacro( FeretDiameter, double );
- const double & GetFeretDiameter() const
- {
- return m_FeretDiameter;
- }
-
- void SetFeretDiameter( const double & v )
- {
- m_FeretDiameter = v;
- }
-
-// itkGetConstMacro( BinaryPrincipalMoments, VectorType );
-// itkSetMacro( BinaryPrincipalMoments, VectorType );
- const VectorType & GetBinaryPrincipalMoments() const
- {
- return m_BinaryPrincipalMoments;
- }
-
- void SetBinaryPrincipalMoments( const VectorType & v )
- {
- m_BinaryPrincipalMoments = v;
- }
-
-// itkGetConstMacro( BinaryPrincipalAxes, MatrixType );
-// itkSetMacro( BinaryPrincipalAxes, MatrixType );
- const MatrixType & GetBinaryPrincipalAxes() const
- {
- return m_BinaryPrincipalAxes;
- }
-
- void SetBinaryPrincipalAxes( const MatrixType & v )
- {
- m_BinaryPrincipalAxes = v;
- }
-
-// itkGetConstMacro( BinaryElongation, double );
-// itkSetMacro( BinaryElongation, double );
- const double & GetBinaryElongation() const
- {
- return m_BinaryElongation;
- }
-
- void SetBinaryElongation( const double & v )
- {
- m_BinaryElongation = v;
- }
-
-// itkGetConstMacro( Perimeter, double );
-// itkSetMacro( Perimeter, double );
- const double & GetPerimeter() const
- {
- return m_Perimeter;
- }
-
- void SetPerimeter( const double & v )
- {
- m_Perimeter = v;
- }
-
-// itkGetConstMacro( Roundness, double );
-// itkSetMacro( Roundness, double );
- const double & GetRoundness() const
- {
- return m_Roundness;
- }
-
- void SetRoundness( const double & v )
- {
- m_Roundness = v;
- }
-
-// itkGetConstMacro( EquivalentRadius, double );
-// itkSetMacro( EquivalentRadius, double );
- const double & GetEquivalentRadius() const
- {
- return m_EquivalentRadius;
- }
-
- void SetEquivalentRadius( const double & v )
- {
- m_EquivalentRadius = v;
- }
-
-// itkGetConstMacro( EquivalentPerimeter, double );
-// itkSetMacro( EquivalentPerimeter, double );
- const double & GetEquivalentPerimeter() const
- {
- return m_EquivalentPerimeter;
- }
-
- void SetEquivalentPerimeter( const double & v )
- {
- m_EquivalentPerimeter = v;
- }
-
-// itkGetConstMacro( EquivalentEllipsoidSize, VectorType );
-// itkSetMacro( EquivalentEllipsoidSize, VectorType );
- const VectorType & GetEquivalentEllipsoidSize() const
- {
- return m_EquivalentEllipsoidSize;
- }
-
- void SetEquivalentEllipsoidSize( const VectorType & v )
- {
- m_EquivalentEllipsoidSize = v;
- }
-
-
-// some helper methods - not really required, but really useful!
-
- /** Affine transform for mapping to and from principal axis */
- typedef AffineTransform<double,itkGetStaticConstMacro(ImageDimension)> AffineTransformType;
- typedef typename AffineTransformType::Pointer AffineTransformPointer;
-
- /** Get the affine transform from principal axes to physical axes
- * This method returns an affine transform which transforms from
- * the principal axes coordinate system to physical coordinates. */
- AffineTransformPointer GetBinaryPrincipalAxesToPhysicalAxesTransform() const
- {
- typename AffineTransformType::MatrixType matrix;
- typename AffineTransformType::OffsetType offset;
- for (unsigned int i = 0; i < ImageDimension; i++)
- {
- offset[i] = m_Centroid[i];
- for (unsigned int j = 0; j < ImageDimension; j++)
- {
- matrix[j][i] = m_BinaryPrincipalAxes[i][j]; // Note the transposition
- }
- }
-
- AffineTransformPointer result = AffineTransformType::New();
-
- result->SetMatrix(matrix);
- result->SetOffset(offset);
-
- return result;
- }
-
- /** Get the affine transform from physical axes to principal axes
- * This method returns an affine transform which transforms from
- * the physical coordinate system to the principal axes coordinate
- * system. */
- AffineTransformPointer GetPhysicalAxesToBinaryPrincipalAxesTransform(void) const
- {
- typename AffineTransformType::MatrixType matrix;
- typename AffineTransformType::OffsetType offset;
- for (unsigned int i = 0; i < ImageDimension; i++)
- {
- offset[i] = m_Centroid[i];
- for (unsigned int j = 0; j < ImageDimension; j++)
- {
- matrix[j][i] = m_BinaryPrincipalAxes[i][j]; // Note the transposition
- }
- }
-
- AffineTransformPointer result = AffineTransformType::New();
- result->SetMatrix(matrix);
- result->SetOffset(offset);
-
- AffineTransformPointer inverse = AffineTransformType::New();
- result->GetInverse(inverse);
-
- return inverse;
- }
-
-
-
- virtual void CopyAttributesFrom( const Self * src )
- {
- Superclass::CopyAttributesFrom( src );
-
- m_Region = src->m_Region;
- m_Size = src->m_Size;
- m_PhysicalSize = src->m_PhysicalSize;
- m_Centroid = src->m_Centroid;
- m_RegionElongation = src->m_RegionElongation;
- m_SizeRegionRatio = src->m_SizeRegionRatio;
- m_SizeOnBorder = src->m_SizeOnBorder;
- m_PhysicalSizeOnBorder = src->m_PhysicalSizeOnBorder;
- m_FeretDiameter = src->m_FeretDiameter;
- m_BinaryPrincipalMoments = src->m_BinaryPrincipalMoments;
- m_BinaryPrincipalAxes = src->m_BinaryPrincipalAxes;
- m_BinaryElongation = src->m_BinaryElongation;
- m_Perimeter = src->m_Perimeter;
- m_Roundness = src->m_Roundness;
- m_EquivalentRadius = src->m_EquivalentRadius;
- m_EquivalentPerimeter = src->m_EquivalentPerimeter;
- m_EquivalentEllipsoidSize = src->m_EquivalentEllipsoidSize;
- }
-
-protected:
- ShapeLabelObject()
- {
- m_Size = 0;
- m_PhysicalSize = 0;
- m_Centroid.Fill(0);
- m_RegionElongation = 0;
- m_SizeRegionRatio = 0;
- m_SizeOnBorder = false;
- m_PhysicalSizeOnBorder = 0;
- m_FeretDiameter = false;
- m_BinaryPrincipalMoments.Fill(0);
- m_BinaryPrincipalAxes.Fill(0);
- m_BinaryElongation = 0;
- m_Perimeter = 0;
- m_Roundness = 0;
- m_EquivalentRadius = 0;
- m_EquivalentPerimeter = 0;
- m_EquivalentEllipsoidSize.Fill(0);
- }
-
-
- void PrintSelf(std::ostream& os, Indent indent) const
- {
- Superclass::PrintSelf( os, indent );
-
- os << indent << "Centroid: " << m_Centroid << std::endl;
- os << indent << "Region: ";
- m_Region.Print( os, indent );
- os << indent << "PhysicalSize: " << m_PhysicalSize << std::endl;
- os << indent << "Size: " << m_Size << std::endl;
- os << indent << "RegionElongation: " << m_RegionElongation << std::endl;
- os << indent << "SizeRegionRatio: " << m_SizeRegionRatio << std::endl;
- os << indent << "SizeOnBorder: " << m_SizeOnBorder << std::endl;
- os << indent << "PhysicalSizeOnBorder: " << m_PhysicalSizeOnBorder << std::endl;
- os << indent << "FeretDiameter: " << m_FeretDiameter << std::endl;
- os << indent << "BinaryPrincipalMoments: " << m_BinaryPrincipalMoments << std::endl;
- os << indent << "BinaryPrincipalAxes: " << std::endl << m_BinaryPrincipalAxes;
- os << indent << "BinaryElongation: " << m_BinaryElongation << std::endl;
- os << indent << "Perimeter: " << m_Perimeter << std::endl;
- os << indent << "Roundness: " << m_Roundness << std::endl;
- os << indent << "EquivalentRadius: " << m_EquivalentRadius << std::endl;
- os << indent << "EquivalentPerimeter: " << m_EquivalentPerimeter << std::endl;
- os << indent << "EquivalentEllipsoidSize: " << m_EquivalentEllipsoidSize << std::endl;
- }
-
-private:
- ShapeLabelObject(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
- RegionType m_Region;
- unsigned long m_Size;
- double m_PhysicalSize;
- CentroidType m_Centroid;
- double m_RegionElongation;
- double m_SizeRegionRatio;
- unsigned long m_SizeOnBorder;
- double m_PhysicalSizeOnBorder;
- double m_FeretDiameter;
- VectorType m_BinaryPrincipalMoments;
- MatrixType m_BinaryPrincipalAxes;
- double m_BinaryElongation;
- double m_Perimeter;
- double m_Roundness;
- double m_EquivalentRadius;
- double m_EquivalentPerimeter;
- VectorType m_EquivalentEllipsoidSize;
-
-};
-
-} // end namespace itk
-
-#endif
diff --git a/Utilities/InsightJournal/itkShapeOpeningLabelMapFilter.h b/Utilities/InsightJournal/itkShapeOpeningLabelMapFilter.h
deleted file mode 100644
index 84aaebb6c5918da1496af7bc6cbfef4749bd0af5..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkShapeOpeningLabelMapFilter.h
+++ /dev/null
@@ -1,135 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkShapeOpeningLabelMapFilter.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 __itkShapeOpeningLabelMapFilter_h
-#define __itkShapeOpeningLabelMapFilter_h
-
-#include "itkInPlaceLabelMapFilter.h"
-
-namespace itk {
-/** \class ShapeOpeningLabelMapFilter
- * \brief remove the objects according to the value of their shape attribute
- *
- * ShapeOpeningLabelMapFilter removes the objects in a label collection 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, BinaryShapeOpeningImageFilter, LabelStatisticsOpeningImageFilter
- * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
- */
-template<class TImage>
-class ITK_EXPORT ShapeOpeningLabelMapFilter :
- public InPlaceLabelMapFilter<TImage>
-{
-public:
- /** Standard class typedefs. */
- typedef ShapeOpeningLabelMapFilter 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 typename LabelObjectType::AttributeType AttributeType;
-
- /** ImageDimension constants */
- itkStaticConstMacro(ImageDimension, unsigned int,
- TImage::ImageDimension);
-
- /** Standard New method. */
- itkNewMacro(Self);
-
- /** Runtime information support. */
- itkTypeMacro(ShapeOpeningLabelMapFilter,
- 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, 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:
- ShapeOpeningLabelMapFilter();
- ~ShapeOpeningLabelMapFilter() {};
-
- void GenerateData();
-
- template <class TAttributeAccessor> void TemplatedGenerateData();
-
- void PrintSelf(std::ostream& os, Indent indent) const;
-
- double m_Lambda;
- bool m_ReverseOrdering;
- AttributeType m_Attribute;
-
-private:
- ShapeOpeningLabelMapFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
-} ; // end of class
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkShapeOpeningLabelMapFilter.txx"
-#endif
-
-#endif
-
-
diff --git a/Utilities/InsightJournal/itkShapeOpeningLabelMapFilter.txx b/Utilities/InsightJournal/itkShapeOpeningLabelMapFilter.txx
deleted file mode 100644
index f2413d78a348c112d6a65156539f1eae3664d5ae..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkShapeOpeningLabelMapFilter.txx
+++ /dev/null
@@ -1,139 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkShapeOpeningLabelMapFilter.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 __itkShapeOpeningLabelMapFilter_txx
-#define __itkShapeOpeningLabelMapFilter_txx
-
-#include "itkShapeOpeningLabelMapFilter.h"
-#include "itkProgressReporter.h"
-
-
-namespace itk {
-
-template <class TImage>
-ShapeOpeningLabelMapFilter<TImage>
-::ShapeOpeningLabelMapFilter()
-{
- m_Lambda = NumericTraits< double >::Zero;
- m_ReverseOrdering = false;
- m_Attribute = LabelObjectType::SIZE;
-}
-
-
-template <class TImage>
-void
-ShapeOpeningLabelMapFilter<TImage>
-::GenerateData()
-{
- switch( m_Attribute )
- {
- case LabelObjectType::SIZE:
- TemplatedGenerateData< typename Functor::SizeLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::PHYSICAL_SIZE:
- TemplatedGenerateData< typename Functor::PhysicalSizeLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::SIZE_REGION_RATIO:
- TemplatedGenerateData< typename Functor::SizeRegionRatioLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::REGION_ELONGATION:
- TemplatedGenerateData< typename Functor::RegionElongationLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::SIZE_ON_BORDER:
- TemplatedGenerateData< typename Functor::SizeOnBorderLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::PHYSICAL_SIZE_ON_BORDER:
- TemplatedGenerateData< typename Functor::PhysicalSizeOnBorderLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::FERET_DIAMETER:
- TemplatedGenerateData< typename Functor::FeretDiameterLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::BINARY_ELONGATION:
- TemplatedGenerateData< typename Functor::BinaryElongationLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::PERIMETER:
- TemplatedGenerateData< typename Functor::PerimeterLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::ROUNDNESS:
- TemplatedGenerateData< typename Functor::RoundnessLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::EQUIVALENT_RADIUS:
- TemplatedGenerateData< typename Functor::EquivalentRadiusLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::EQUIVALENT_PERIMETER:
- TemplatedGenerateData< typename Functor::EquivalentPerimeterLabelObjectAccessor< LabelObjectType > >();
- break;
- default:
- itkExceptionMacro(<< "Unknown attribute type");
- break;
- }
-}
-
-template <class TImage>
-template <class TAttributeAccessor>
-void
-ShapeOpeningLabelMapFilter<TImage>
-::TemplatedGenerateData()
-{
- // Allocate the output
- this->AllocateOutputs();
-
- ImageType * output = this->GetOutput();
-
- TAttributeAccessor 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;
-
- if( ( !m_ReverseOrdering && accessor( labelObject ) < m_Lambda )
- || ( m_ReverseOrdering && 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>
-void
-ShapeOpeningLabelMapFilter<TImage>
-::PrintSelf(std::ostream &os, Indent indent) const
-{
- Superclass::PrintSelf(os, indent);
-
- os << indent << "ReverseOrdering: " << m_ReverseOrdering << std::endl;
- os << indent << "Lambda: " << m_Lambda << std::endl;
- os << indent << "Attribute: " << LabelObjectType::GetNameFromAttribute(m_Attribute) << " (" << m_Attribute << ")" << std::endl;
-}
-
-}// end namespace itk
-#endif
diff --git a/Utilities/InsightJournal/itkShapeRelabelImageFilter.h b/Utilities/InsightJournal/itkShapeRelabelImageFilter.h
deleted file mode 100644
index 140ee9b668a0fab068233b61eb78ffdae9829ddb..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkShapeRelabelImageFilter.h
+++ /dev/null
@@ -1,161 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkShapeRelabelImageFilter.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 __itkShapeRelabelImageFilter_h
-#define __itkShapeRelabelImageFilter_h
-
-#include "itkImageToImageFilter.h"
-#include "itkShapeLabelObject.h"
-#include "itkLabelMap.h"
-#include "itkLabelImageToLabelMapFilter.h"
-#include "itkShapeLabelMapFilter.h"
-#include "itkShapeRelabelLabelMapFilter.h"
-#include "itkLabelMapToLabelImageFilter.h"
-
-
-namespace itk {
-
-/** \class ShapeRelabelImageFilter
- * \brief relabel objects according to their shape attributes
- *
- * ShapeRelabelImageFilter relabel a labeled image according to the shape attributes 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 ShapeLabelObject, RelabelComponentImageFilter
- * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
- */
-template<class TInputImage>
-class ITK_EXPORT ShapeRelabelImageFilter :
- public ImageToImageFilter<TInputImage, TInputImage>
-{
-public:
- /** Standard class typedefs. */
- typedef ShapeRelabelImageFilter 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<InputImagePixelType, ImageDimension> LabelObjectType;
- typedef typename itk::LabelMap< LabelObjectType > LabelMapType;
- typedef typename itk::LabelImageToLabelMapFilter< InputImageType, LabelMapType > LabelizerType;
- typedef typename itk::ShapeLabelMapFilter< LabelMapType > LabelObjectValuatorType;
- typedef typename LabelObjectType::AttributeType AttributeType;
- typedef typename itk::ShapeRelabelLabelMapFilter< LabelMapType > RelabelType;
- typedef typename itk::LabelMapToLabelImageFilter< LabelMapType, OutputImageType > BinarizerType;
-
- /** Standard New method. */
- itkNewMacro(Self);
-
- /** Runtime information support. */
- itkTypeMacro(ShapeRelabelImageFilter,
- 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 );
-
- /**
- * Set/Get the attribute to use. Default is "Size".
- */
- itkGetConstMacro( Attribute, AttributeType );
- itkSetMacro( Attribute, AttributeType );
- void SetAttribute( const std::string & s )
- {
- this->SetAttribute( LabelObjectType::GetAttributeFromName( s ) );
- }
-
-
-protected:
- ShapeRelabelImageFilter();
- ~ShapeRelabelImageFilter() {};
- void PrintSelf(std::ostream& os, Indent indent) const;
-
- /** ShapeRelabelImageFilter needs the entire input be
- * available. Thus, it needs to provide an implementation of
- * GenerateInputRequestedRegion(). */
- void GenerateInputRequestedRegion() ;
-
- /** ShapeRelabelImageFilter will produce the entire output. */
- void EnlargeOutputRequestedRegion(DataObject *itkNotUsed(output));
-
- /** Single-threaded version of GenerateData. This filter delegates
- * to GrayscaleGeodesicErodeImageFilter. */
- void GenerateData();
-
-private:
- ShapeRelabelImageFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
- OutputImagePixelType m_BackgroundValue;
- bool m_ReverseOrdering;
- AttributeType m_Attribute;
-} ; // end of class
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkShapeRelabelImageFilter.txx"
-#endif
-
-#endif
-
-
diff --git a/Utilities/InsightJournal/itkShapeRelabelImageFilter.txx b/Utilities/InsightJournal/itkShapeRelabelImageFilter.txx
deleted file mode 100644
index c9010a9fe0fcff7f21061536abc3396d0a15d74a..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkShapeRelabelImageFilter.txx
+++ /dev/null
@@ -1,125 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkShapeRelabelImageFilter.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 __itkShapeRelabelImageFilter_txx
-#define __itkShapeRelabelImageFilter_txx
-
-#include "itkShapeRelabelImageFilter.h"
-#include "itkProgressAccumulator.h"
-
-
-namespace itk {
-
-template<class TInputImage>
-ShapeRelabelImageFilter<TInputImage>
-::ShapeRelabelImageFilter()
-{
- m_BackgroundValue = NumericTraits<OutputImagePixelType>::NonpositiveMin();
- m_ReverseOrdering = false;
- m_Attribute = LabelObjectType::SIZE;
-}
-
-template<class TInputImage>
-void
-ShapeRelabelImageFilter<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
-ShapeRelabelImageFilter<TInputImage>
-::EnlargeOutputRequestedRegion(DataObject *)
-{
- this->GetOutput()
- ->SetRequestedRegion( this->GetOutput()->GetLargestPossibleRegion() );
-}
-
-
-template<class TInputImage>
-void
-ShapeRelabelImageFilter<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->SetBackgroundValue( m_BackgroundValue );
- labelizer->SetNumberOfThreads( this->GetNumberOfThreads() );
- progress->RegisterInternalFilter(labelizer, .3f);
-
- typename LabelObjectValuatorType::Pointer valuator = LabelObjectValuatorType::New();
- valuator->SetInput( labelizer->GetOutput() );
- valuator->SetLabelImage( this->GetInput() );
- 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 RelabelType::Pointer opening = RelabelType::New();
- opening->SetInput( valuator->GetOutput() );
- 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->SetNumberOfThreads( this->GetNumberOfThreads() );
- progress->RegisterInternalFilter(binarizer, .2f);
-
- binarizer->GraftOutput( this->GetOutput() );
- binarizer->Update();
- this->GraftOutput( binarizer->GetOutput() );
-}
-
-
-template<class TInputImage>
-void
-ShapeRelabelImageFilter<TInputImage>
-::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;
- os << indent << "Attribute: " << LabelObjectType::GetNameFromAttribute(m_Attribute) << " (" << m_Attribute << ")" << std::endl;
-}
-
-}// end namespace itk
-#endif
diff --git a/Utilities/InsightJournal/itkShapeRelabelLabelMapFilter.h b/Utilities/InsightJournal/itkShapeRelabelLabelMapFilter.h
deleted file mode 100644
index 3dbbd57794c368f69b2d6b71400f170acb1b9fdb..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkShapeRelabelLabelMapFilter.h
+++ /dev/null
@@ -1,125 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkShapeRelabelLabelMapFilter.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 __itkShapeRelabelLabelMapFilter_h
-#define __itkShapeRelabelLabelMapFilter_h
-
-#include "itkInPlaceLabelMapFilter.h"
-
-namespace itk {
-/** \class ShapeRelabelLabelMapFilter
- * \brief relabel objects according to their shape attributes
- *
- * ShapeRelabelImageFilter relabel a label collection image according to the shape attributes 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 ShapeLabelObject, RelabelComponentImageFilter
- * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
- */
-template<class TImage >
-class ITK_EXPORT ShapeRelabelLabelMapFilter :
- public InPlaceLabelMapFilter<TImage>
-{
-public:
- /** Standard class typedefs. */
- typedef ShapeRelabelLabelMapFilter 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 typename LabelObjectType::AttributeType AttributeType;
-
- /** ImageDimension constants */
- itkStaticConstMacro(ImageDimension, unsigned int,
- TImage::ImageDimension);
-
- /** Standard New method. */
- itkNewMacro(Self);
-
- /** Runtime information support. */
- itkTypeMacro(ShapeRelabelLabelMapFilter,
- 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 );
-
- /**
- * Set/Get the attribute to use. Default is "Size".
- */
- itkGetConstMacro( Attribute, AttributeType );
- itkSetMacro( Attribute, AttributeType );
- void SetAttribute( const std::string & s )
- {
- this->SetAttribute( LabelObjectType::GetAttributeFromName( s ) );
- }
-
-
-protected:
- ShapeRelabelLabelMapFilter();
- ~ShapeRelabelLabelMapFilter() {};
-
- void GenerateData();
-
- template <class TAttributeAccessor> void TemplatedGenerateData();
-
- void PrintSelf(std::ostream& os, Indent indent) const;
-
- bool m_ReverseOrdering;
- AttributeType m_Attribute;
-
-private:
- ShapeRelabelLabelMapFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
-} ; // end of class
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkShapeRelabelLabelMapFilter.txx"
-#endif
-
-#endif
-
-
diff --git a/Utilities/InsightJournal/itkShapeRelabelLabelMapFilter.txx b/Utilities/InsightJournal/itkShapeRelabelLabelMapFilter.txx
deleted file mode 100644
index fa6957413363301f60f8cbcc4a2d3fd5ae6a68bb..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkShapeRelabelLabelMapFilter.txx
+++ /dev/null
@@ -1,161 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkShapeRelabelLabelMapFilter.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 __itkShapeRelabelLabelMapFilter_txx
-#define __itkShapeRelabelLabelMapFilter_txx
-
-#include "itkShapeRelabelLabelMapFilter.h"
-#include "itkProgressReporter.h"
-
-
-namespace itk {
-
-template <class TImage>
-ShapeRelabelLabelMapFilter<TImage>
-::ShapeRelabelLabelMapFilter()
-{
- m_ReverseOrdering = false;
- m_Attribute = LabelObjectType::SIZE;
-}
-
-
-template <class TImage>
-void
-ShapeRelabelLabelMapFilter<TImage>
-::GenerateData()
-{
- switch( m_Attribute )
- {
- case LabelObjectType::SIZE:
- TemplatedGenerateData< typename Functor::SizeLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::PHYSICAL_SIZE:
- TemplatedGenerateData< typename Functor::PhysicalSizeLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::SIZE_REGION_RATIO:
- TemplatedGenerateData< typename Functor::SizeRegionRatioLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::REGION_ELONGATION:
- TemplatedGenerateData< typename Functor::RegionElongationLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::SIZE_ON_BORDER:
- TemplatedGenerateData< typename Functor::SizeOnBorderLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::PHYSICAL_SIZE_ON_BORDER:
- TemplatedGenerateData< typename Functor::PhysicalSizeOnBorderLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::FERET_DIAMETER:
- TemplatedGenerateData< typename Functor::FeretDiameterLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::BINARY_ELONGATION:
- TemplatedGenerateData< typename Functor::BinaryElongationLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::PERIMETER:
- TemplatedGenerateData< typename Functor::PerimeterLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::ROUNDNESS:
- TemplatedGenerateData< typename Functor::RoundnessLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::EQUIVALENT_RADIUS:
- TemplatedGenerateData< typename Functor::EquivalentRadiusLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::EQUIVALENT_PERIMETER:
- TemplatedGenerateData< typename Functor::EquivalentPerimeterLabelObjectAccessor< LabelObjectType > >();
- break;
- default:
- itkExceptionMacro(<< "Unknown attribute type");
- break;
- }
-}
-
-
-template <class TImage>
-template <class TAttributeAccessor>
-void
-ShapeRelabelLabelMapFilter<TImage>
-::TemplatedGenerateData()
-{
- // 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 )
- {
- Functor::LabelObjectReverseComparator< LabelObjectType, TAttributeAccessor > comparator;
- std::sort( labelObjects.begin(), labelObjects.end(), comparator );
- }
- else
- {
- Functor::LabelObjectComparator< LabelObjectType, TAttributeAccessor > 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>
-void
-ShapeRelabelLabelMapFilter<TImage>
-::PrintSelf(std::ostream& os, Indent indent) const
-{
- Superclass::PrintSelf(os,indent);
-
- 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/itkStatisticsKeepNObjectsLabelMapFilter.h b/Utilities/InsightJournal/itkStatisticsKeepNObjectsLabelMapFilter.h
deleted file mode 100644
index c3996617e0a636ce7b8df56a856e35b1079198b4..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkStatisticsKeepNObjectsLabelMapFilter.h
+++ /dev/null
@@ -1,101 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkStatisticsKeepNObjectsLabelMapFilter.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 __itkStatisticsKeepNObjectsLabelMapFilter_h
-#define __itkStatisticsKeepNObjectsLabelMapFilter_h
-
-#include "itkShapeKeepNObjectsLabelMapFilter.h"
-#include "itkStatisticsLabelObject.h"
-
-namespace itk {
-/** \class StatisticsKeepNObjectsLabelMapFilter
- * \brief keep N objects according to their statistics attributes
- *
- * StatisticsKeepNObjectsLabelMapFilter keep the N objects in a label collection 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, BinaryStatisticsKeepNObjectsImageFilter, LabelShapeKeepNObjectsImageFilter
- * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
- */
-template<class TImage>
-class ITK_EXPORT StatisticsKeepNObjectsLabelMapFilter :
- public ShapeKeepNObjectsLabelMapFilter<TImage>
-{
-public:
- /** Standard class typedefs. */
- typedef StatisticsKeepNObjectsLabelMapFilter Self;
- typedef ShapeKeepNObjectsLabelMapFilter<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 typename LabelObjectType::AttributeType AttributeType;
-
- /** ImageDimension constants */
- itkStaticConstMacro(ImageDimension, unsigned int,
- TImage::ImageDimension);
-
- /** Standard New method. */
- itkNewMacro(Self);
-
- /** Runtime information support. */
- itkTypeMacro(StatisticsKeepNObjectsLabelMapFilter,
- ShapeKeepNObjectsLabelMapFilter);
-
-#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
-protected:
- StatisticsKeepNObjectsLabelMapFilter();
- ~StatisticsKeepNObjectsLabelMapFilter() {};
-
- void GenerateData();
-
- template <class TAttributeAccessor> void TemplatedGenerateData();
-
-private:
- StatisticsKeepNObjectsLabelMapFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
-} ; // end of class
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkStatisticsKeepNObjectsLabelMapFilter.txx"
-#endif
-
-#endif
-
-
diff --git a/Utilities/InsightJournal/itkStatisticsKeepNObjectsLabelMapFilter.txx b/Utilities/InsightJournal/itkStatisticsKeepNObjectsLabelMapFilter.txx
deleted file mode 100644
index 435ba468bceabd866fafa5215ad368f7be71e5f8..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkStatisticsKeepNObjectsLabelMapFilter.txx
+++ /dev/null
@@ -1,135 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkStatisticsKeepNObjectsLabelMapFilter.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 __itkStatisticsKeepNObjectsLabelMapFilter_txx
-#define __itkStatisticsKeepNObjectsLabelMapFilter_txx
-
-#include "itkStatisticsKeepNObjectsLabelMapFilter.h"
-#include "itkProgressReporter.h"
-#include "itkLabelObjectUtils.h"
-
-
-namespace itk {
-
-template <class TImage>
-StatisticsKeepNObjectsLabelMapFilter<TImage>
-::StatisticsKeepNObjectsLabelMapFilter()
-{
- this->m_Attribute = LabelObjectType::MEAN;
-}
-
-
-template <class TImage>
-void
-StatisticsKeepNObjectsLabelMapFilter<TImage>
-::GenerateData()
-{
- switch( this->m_Attribute )
- {
- case LabelObjectType::MINIMUM:
- TemplatedGenerateData< typename Functor::MinimumLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::MAXIMUM:
- TemplatedGenerateData< typename Functor::MaximumLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::MEAN:
- TemplatedGenerateData< typename Functor::MeanLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::SUM:
- TemplatedGenerateData< typename Functor::SumLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::SIGMA:
- TemplatedGenerateData< typename Functor::SigmaLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::VARIANCE:
- TemplatedGenerateData< typename Functor::VarianceLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::MEDIAN:
- TemplatedGenerateData< typename Functor::MedianLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::KURTOSIS:
- TemplatedGenerateData< typename Functor::KurtosisLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::SKEWNESS:
- TemplatedGenerateData< typename Functor::SkewnessLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::ELONGATION:
- TemplatedGenerateData< typename Functor::ElongationLabelObjectAccessor< LabelObjectType > >();
- break;
- default:
- Superclass::GenerateData();
- break;
- }
-}
-
-
-template <class TImage>
-template <class TAttributeAccessor>
-void
-StatisticsKeepNObjectsLabelMapFilter<TImage>
-::TemplatedGenerateData()
-{
- // 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( this->m_NumberOfObjects < labelObjectContainer.size() )
- {
- typename VectorType::iterator end = labelObjects.begin() + this->m_NumberOfObjects;
- if( this->m_ReverseOrdering )
- {
- Functor::LabelObjectReverseComparator< LabelObjectType, TAttributeAccessor > comparator;
- std::nth_element( labelObjects.begin(), end, labelObjects.end(), comparator );
- }
- else
- {
- Functor::LabelObjectComparator< LabelObjectType, TAttributeAccessor > 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();
- }
- }
-}
-
-}// end namespace itk
-#endif
diff --git a/Utilities/InsightJournal/itkStatisticsLabelMapFilter.h b/Utilities/InsightJournal/itkStatisticsLabelMapFilter.h
deleted file mode 100644
index ee81b7de6d0bc35f3cc5985e4b31258066fe8513..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkStatisticsLabelMapFilter.h
+++ /dev/null
@@ -1,156 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkStatisticsLabelMapFilter.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 __itkStatisticsLabelMapFilter_h
-#define __itkStatisticsLabelMapFilter_h
-
-#include "itkShapeLabelMapFilter.h"
-
-namespace itk {
-/** \class StatisticsLabelMapFilter
- * \brief The valuator class for the ShapeLabelObject
- *
- * StatisticsCollectionImageFilter can be used to set the attributes values
- * of the StatisticsLabelObject in a LabelMap.
- *
- * \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 TFeatureImage>
-class ITK_EXPORT StatisticsLabelMapFilter :
- public ShapeLabelMapFilter<TImage>
-{
-public:
- /** Standard class typedefs. */
- typedef StatisticsLabelMapFilter Self;
- typedef ShapeLabelMapFilter<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::PointType PointType;
- typedef typename ImageType::LabelObjectType LabelObjectType;
- typedef typename LabelObjectType::MatrixType MatrixType;
- typedef typename LabelObjectType::VectorType VectorType;
-
- typedef TFeatureImage FeatureImageType;
- typedef typename FeatureImageType::Pointer FeatureImagePointer;
- typedef typename FeatureImageType::ConstPointer FeatureImageConstPointer;
- typedef typename FeatureImageType::PixelType FeatureImagePixelType;
-
- /** ImageDimension constants */
- itkStaticConstMacro(ImageDimension, unsigned int,
- TImage::ImageDimension);
-
- /** Standard New method. */
- itkNewMacro(Self);
-
- /** Runtime information support. */
- itkTypeMacro(StatisticsLabelMapFilter,
- ShapeLabelMapFilter);
-
-#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 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(TImage *input)
- {
- this->SetInput( input );
- }
-
- /** Set the feature image */
- void SetInput2(TFeatureImage *input)
- {
- this->SetFeatureImage( input );
- }
-
- /**
- * Set/Get whether the histogram should be attached to the label object or not.
- * This option defaults to `true`, but because the histogram may take a lot of memory
- * compared to the other attributes, this option is useful to reduce the memory usage
- * when the histogram is not required.
- */
- itkSetMacro(ComputeHistogram, bool);
- itkGetConstReferenceMacro(ComputeHistogram, bool);
- itkBooleanMacro(ComputeHistogram);
-
- /**
- * Set/Get the number of bins in the histogram. Note that the histogram is used
- * to compute the median value, and that this option may have an effect on the
- * value of the median.
- */
- itkSetMacro(NumberOfBins, unsigned int);
- itkGetConstReferenceMacro(NumberOfBins, unsigned int);
-
-
-protected:
- StatisticsLabelMapFilter();
- ~StatisticsLabelMapFilter() {};
-
- virtual void ThreadedGenerateData( LabelObjectType * labelObject );
-
- virtual void BeforeThreadedGenerateData();
-
- void PrintSelf(std::ostream& os, Indent indent) const;
-
-private:
- StatisticsLabelMapFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
- FeatureImagePixelType m_Minimum;
- FeatureImagePixelType m_Maximum;
- unsigned int m_NumberOfBins;
- bool m_ComputeHistogram;
-
-} ; // end of class
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkStatisticsLabelMapFilter.txx"
-#endif
-
-#endif
-
-
diff --git a/Utilities/InsightJournal/itkStatisticsLabelMapFilter.txx b/Utilities/InsightJournal/itkStatisticsLabelMapFilter.txx
deleted file mode 100644
index 6a784b3a18b198ee6fa91cfd90d91b334af93e65..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkStatisticsLabelMapFilter.txx
+++ /dev/null
@@ -1,290 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkStatisticsLabelMapFilter.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 __itkStatisticsLabelMapFilter_txx
-#define __itkStatisticsLabelMapFilter_txx
-
-#include "itkStatisticsLabelMapFilter.h"
-#include "itkMinimumMaximumImageCalculator.h"
-#include "itkProgressReporter.h"
-#include "vnl/algo/vnl_real_eigensystem.h"
-#include "vnl/algo/vnl_symmetric_eigensystem.h"
-
-
-namespace itk {
-
-template <class TImage, class TFeatureImage>
-StatisticsLabelMapFilter<TImage, TFeatureImage>
-::StatisticsLabelMapFilter()
-{
- m_NumberOfBins = 128;
- m_ComputeHistogram = true;
- this->SetNumberOfRequiredInputs(2);
-}
-
-
-template <class TImage, class TFeatureImage>
-void
-StatisticsLabelMapFilter<TImage, TFeatureImage>
-::BeforeThreadedGenerateData()
-{
- Superclass::BeforeThreadedGenerateData();
-
- // get the min and max of the feature image, to use those value as the bounds of our
- // histograms
- typedef MinimumMaximumImageCalculator< FeatureImageType > MinMaxCalculatorType;
- typename MinMaxCalculatorType::Pointer minMax = MinMaxCalculatorType::New();
- minMax->SetImage( this->GetFeatureImage() );
- minMax->Compute();
-
- m_Minimum = minMax->GetMinimum();
- m_Maximum = minMax->GetMaximum();
-
-}
-
-
-template <class TImage, class TFeatureImage>
-void
-StatisticsLabelMapFilter<TImage, TFeatureImage>
-::ThreadedGenerateData( LabelObjectType * labelObject )
-{
- Superclass::ThreadedGenerateData( labelObject );
-
- ImageType * output = this->GetOutput();
- const FeatureImageType * featureImage = this->GetFeatureImage();
-
- typedef typename LabelObjectType::HistogramType HistogramType;
-
- typename HistogramType::SizeType histogramSize;
- histogramSize.Fill( m_NumberOfBins );
- typename HistogramType::MeasurementVectorType featureImageMin;
- featureImageMin.Fill( m_Minimum );
- typename HistogramType::MeasurementVectorType featureImageMax;
- featureImageMax.Fill( m_Maximum );
-
- typename HistogramType::Pointer histogram = HistogramType::New();
- histogram->SetClipBinsAtEnds( false );
- histogram->Initialize( histogramSize, featureImageMin, featureImageMax );
-
- typename LabelObjectType::LineContainerType::const_iterator lit;
- typename LabelObjectType::LineContainerType & lineContainer = labelObject->GetLineContainer();
-
- FeatureImagePixelType min = NumericTraits< FeatureImagePixelType >::max();
- FeatureImagePixelType max = NumericTraits< FeatureImagePixelType >::NonpositiveMin();
- double sum = 0;
- double sum2 = 0;
- double sum3 = 0;
- double sum4 = 0;
- IndexType minIdx;
- minIdx.Fill( 0 );
- IndexType maxIdx;
- maxIdx.Fill( 0 );
- PointType centerOfGravity;
- centerOfGravity.Fill( 0 );
- MatrixType centralMoments;
- centralMoments.Fill( 0 );
- MatrixType principalAxes;
- principalAxes.Fill( 0 );
- VectorType principalMoments;
- principalMoments.Fill( 0 );
-
- // iterate over all the lines
- for( lit = lineContainer.begin(); lit != lineContainer.end(); lit++ )
- {
- const IndexType & firstIdx = lit->GetIndex();
- unsigned long length = lit->GetLength();
-
- typename HistogramType::MeasurementVectorType mv;
- long endIdx0 = firstIdx[0] + length;
- for( IndexType idx = firstIdx; idx[0]<endIdx0; idx[0]++)
- {
- const FeatureImagePixelType & v = featureImage->GetPixel( idx );
- mv[0] = v;
- histogram->IncreaseFrequency( mv, 1 );
-
- // update min and max
- if( v <= min )
- {
- min = v;
- minIdx = idx;
- }
- if( v >= max )
- {
- max = v;
- maxIdx = idx;
- }
-
- //increase the sums
- sum += v;
- sum2 += vcl_pow( (double)v, 2 );
- sum3 += vcl_pow( (double)v, 3 );
- sum4 += vcl_pow( (double)v, 4 );
-
- // moments
- PointType physicalPosition;
- output->TransformIndexToPhysicalPoint(idx, physicalPosition);
- for(unsigned int i=0; i<ImageDimension; i++)
- {
- centerOfGravity[i] += physicalPosition[i] * v;
- centralMoments[i][i] += v * physicalPosition[i] * physicalPosition[i];
- for(unsigned int j=i+1; j<ImageDimension; j++)
- {
- double weight = v * physicalPosition[i] * physicalPosition[j];
- centralMoments[i][j] += weight;
- centralMoments[j][i] += weight;
- }
- }
-
- }
- }
-
- // final computations
- const typename HistogramType::FrequencyType & totalFreq = histogram->GetTotalFrequency();
- double mean = sum / totalFreq;
- double variance = ( sum2 - ( vcl_pow( sum, 2 ) / totalFreq ) ) / ( totalFreq - 1 );
- double sigma = vcl_sqrt( variance );
- double mean2 = mean * mean;
- double skewness = ( ( sum3 - 3.0 * mean * sum2) / totalFreq + 2.0 * mean * mean2 ) / ( variance * sigma );
- double kurtosis = ( ( sum4 - 4.0 * mean * sum3 + 6.0 * mean2 * sum2) / totalFreq - 3.0 * mean2 * mean2 ) / ( variance * variance ) - 3.0;
-
- // the median
- double median = 0;
- double count = 0; // will not be fully set, so do not use later !
- for( unsigned long i=0;
- i<histogram->Size();
- i++)
- {
- count += histogram->GetFrequency( i );
-
- if( count >= ( totalFreq / 2 ) )
- {
- median = histogram->GetMeasurementVector( i )[0];
- break;
- }
- }
-
- double elongation = 0;
- if( sum != 0 )
- {
- // Normalize using the total mass
- for(unsigned int i=0; i<ImageDimension; i++)
- {
- centerOfGravity[i] /= sum;
- for(unsigned int j=0; j<ImageDimension; j++)
- {
- centralMoments[i][j] /= sum;
- }
- }
-
- // Center the second order moments
- for(unsigned int i=0; i<ImageDimension; i++)
- {
- for(unsigned int j=0; j<ImageDimension; j++)
- {
- centralMoments[i][j] -= centerOfGravity[i] * centerOfGravity[j];
- }
- }
-
- // Compute principal moments and axes
- vnl_symmetric_eigensystem<double> eigen( centralMoments.GetVnlMatrix() );
- vnl_diag_matrix<double> pm = eigen.D;
- for(unsigned int i=0; i<ImageDimension; i++)
- {
- // principalMoments[i] = 4 * vcl_sqrt( pm(i,i) );
- principalMoments[i] = pm(i,i);
- }
- principalAxes = eigen.V.transpose();
-
- // Add a final reflection if needed for a proper rotation,
- // by multiplying the last row by the determinant
- vnl_real_eigensystem eigenrot( principalAxes.GetVnlMatrix() );
- vnl_diag_matrix< vcl_complex<double> > eigenval = eigenrot.D;
- vcl_complex<double> det( 1.0, 0.0 );
-
- for(unsigned int i=0; i<ImageDimension; i++)
- {
- det *= eigenval( i, i );
- }
-
- for(unsigned int i=0; i<ImageDimension; i++)
- {
- principalAxes[ ImageDimension-1 ][i] *= std::real( det );
- }
-
- if( principalMoments[0] != 0 )
- {
- // elongation = principalMoments[ImageDimension-1] / principalMoments[0];
- elongation = vcl_sqrt(principalMoments[ImageDimension-1] / principalMoments[0]);
- }
- }
- else
- {
- // can't compute anything in that case - just set everything to a default value
- // Normalize using the total mass
- for(unsigned int i=0; i<ImageDimension; i++)
- {
- centerOfGravity[i] = 0;
- principalMoments[i] = 0;
- for(unsigned int j=0; j<ImageDimension; j++)
- {
- principalAxes[i][j] = 0;
- }
- }
- }
-
- // finally put the values in the label object
- labelObject->SetMinimum( (double)min );
- labelObject->SetMaximum( (double)max );
- labelObject->SetSum( sum );
- labelObject->SetMean( mean );
- labelObject->SetMedian( median );
- labelObject->SetVariance( variance );
- labelObject->SetSigma( sigma );
- labelObject->SetMinimumIndex( minIdx );
- labelObject->SetMaximumIndex( maxIdx );
- labelObject->SetCenterOfGravity( centerOfGravity );
- labelObject->SetPrincipalAxes( principalAxes );
- labelObject->SetPrincipalMoments( principalMoments );
-// labelObject->SetCentralMoments( centralMoments );
- labelObject->SetSkewness( skewness );
- labelObject->SetKurtosis( kurtosis );
- labelObject->SetElongation( elongation );
- if( m_ComputeHistogram )
- {
- labelObject->SetHistogram( histogram );
- }
-
-// std::cout << std::endl;
-// labelObject->Print( std::cout );
-// std::cout << std::endl;
-
-}
-
-
-template <class TImage, class TFeatureImage>
-void
-StatisticsLabelMapFilter<TImage, TFeatureImage>
-::PrintSelf(std::ostream& os, Indent indent) const
-{
- Superclass::PrintSelf(os,indent);
-
- os << indent << "ComputeHistogram: " << m_ComputeHistogram << std::endl;
- os << indent << "NumberOfBins: " << m_NumberOfBins << std::endl;
-}
-
-
-}// end namespace itk
-#endif
diff --git a/Utilities/InsightJournal/itkStatisticsLabelObject.h b/Utilities/InsightJournal/itkStatisticsLabelObject.h
deleted file mode 100644
index a6c59cdf6ecb791f75c61302cdb64807a351139d..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkStatisticsLabelObject.h
+++ /dev/null
@@ -1,827 +0,0 @@
-/*=========================================================================
-
- 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 __itkStatisticsLabelObject_h
-#define __itkStatisticsLabelObject_h
-
-#include "itkShapeLabelObject.h"
-#include "itkHistogram.h"
-
-namespace itk
-{
-
-
-namespace Functor {
-
-template< class TLabelObject >
-class ITK_EXPORT MinimumLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef double AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetMinimum();
- }
-};
-
-template< class TLabelObject >
-class ITK_EXPORT MaximumLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef double AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetMaximum();
- }
-};
-
-template< class TLabelObject >
-class ITK_EXPORT MeanLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef double AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetMean();
- }
-};
-
-template< class TLabelObject >
-class ITK_EXPORT SumLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef double AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetSum();
- }
-};
-
-template< class TLabelObject >
-class ITK_EXPORT SigmaLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef double AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetSigma();
- }
-};
-
-template< class TLabelObject >
-class ITK_EXPORT VarianceLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef double AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetVariance();
- }
-};
-
-template< class TLabelObject >
-class ITK_EXPORT MedianLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef double AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetMedian();
- }
-};
-
-template< class TLabelObject >
-class ITK_EXPORT MaximumIndexLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef typename LabelObjectType::IndexType AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetMaximumIndex();
- }
-};
-
-template< class TLabelObject >
-class ITK_EXPORT MinimumIndexLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef typename LabelObjectType::IndexType AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetMinimumIndex();
- }
-};
-
-template< class TLabelObject >
-class ITK_EXPORT CenterOfGravityLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef typename LabelObjectType::PointType AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetCenterOfGravity();
- }
-};
-
-
-/*template< class TLabelObject >
-class ITK_EXPORT CentralMomentsLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef typename LabelObjectType::MatrixType AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetCentralMoments();
- }
-};*/
-
-template< class TLabelObject >
-class ITK_EXPORT PrincipalMomentsLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef typename LabelObjectType::VectorType AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetPrincipalMoments();
- }
-};
-
-template< class TLabelObject >
-class ITK_EXPORT PrincipalAxesLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef typename LabelObjectType::MatrixType AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetPrincipalAxes();
- }
-};
-
-template< class TLabelObject >
-class ITK_EXPORT KurtosisLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef double AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetKurtosis();
- }
-};
-
-template< class TLabelObject >
-class ITK_EXPORT SkewnessLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef double AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetSkewness();
- }
-};
-
-template< class TLabelObject >
-class ITK_EXPORT ElongationLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef double AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetElongation();
- }
-};
-
-template< class TLabelObject >
-class ITK_EXPORT HistogramLabelObjectAccessor
-{
-public:
- typedef TLabelObject LabelObjectType;
- typedef typename LabelObjectType::HistogramType * AttributeValueType;
-
- inline const AttributeValueType operator()( const LabelObjectType * labelObject )
- {
- return labelObject->GetHistogram();
- }
-};
-
-}
-
-
-/** \class ShapeLabelObject
- * \brief A Label object to store the common attributes related to the statistics of the object
- *
- * StatisticsLabelObject stores the common attributes related to the statistics of the object
- *
- * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
- *
- * \ingroup DataRepresentation
- */
-template < class TLabel, unsigned int VImageDimension >
-class ITK_EXPORT StatisticsLabelObject : public ShapeLabelObject< TLabel, VImageDimension >
-{
-public:
- /** Standard class typedefs */
- typedef StatisticsLabelObject Self;
- typedef ShapeLabelObject< 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(StatisticsLabelObject, LabelObject);
-
- typedef LabelMap< Self > LabelMapType;
-
- itkStaticConstMacro(ImageDimension, unsigned int, VImageDimension);
-
- typedef typename Superclass::IndexType IndexType;
-
- typedef Point< double, ImageDimension > PointType;
-
- typedef TLabel LabelType;
-
- typedef typename Superclass::LineType LineType;
-
- typedef typename Superclass::LengthType LengthType;
-
- typedef typename Superclass::LineContainerType LineContainerType;
-
- typedef Matrix< double, ImageDimension, ImageDimension > MatrixType;
-
- typedef Vector< double, ImageDimension > VectorType;
-
- typedef typename itk::Statistics::Histogram< double > HistogramType;
-
- typedef typename Superclass::AttributeType AttributeType;
- static const AttributeType MINIMUM=100;
- static const AttributeType MAXIMUM=101;
- static const AttributeType MEAN=102;
- static const AttributeType SUM=103;
- static const AttributeType SIGMA=104;
- static const AttributeType VARIANCE=105;
- static const AttributeType MEDIAN=106;
- static const AttributeType MAXIMUM_INDEX=107;
- static const AttributeType MINIMUM_INDEX=108;
- static const AttributeType CENTER_OF_GRAVITY=109;
-// static const AttributeType CENTRAL_MOMENTS=110;
- static const AttributeType PRINCIPAL_MOMENTS=111;
- static const AttributeType PRINCIPAL_AXES=112;
- static const AttributeType KURTOSIS=113;
- static const AttributeType SKEWNESS=114;
- static const AttributeType ELONGATION=115;
- static const AttributeType HISTOGRAM=116;
-
- static AttributeType GetAttributeFromName( const std::string & s )
- {
- if( s == "Minimum" )
- {
- return MINIMUM;
- }
- else if( s == "Maximum" )
- {
- return MAXIMUM;
- }
- else if( s == "Mean" )
- {
- return MEAN;
- }
- else if( s == "Sum" )
- {
- return SUM;
- }
- else if( s == "Sigma" )
- {
- return SIGMA;
- }
- else if( s == "Variance" )
- {
- return VARIANCE;
- }
- else if( s == "Median" )
- {
- return MEDIAN;
- }
- else if( s == "MaximumIndex" )
- {
- return MAXIMUM_INDEX;
- }
- else if( s == "MinimumIndex" )
- {
- return MINIMUM_INDEX;
- }
- else if( s == "CenterOfGravity" )
- {
- return CENTER_OF_GRAVITY;
- }
-/* else if( s == "CentralMoments" )
- {
- return CENTRAL_MOMENTS;
- }*/
- else if( s == "PrincipalMoments" )
- {
- return PRINCIPAL_MOMENTS;
- }
- else if( s == "PrincipalAxes" )
- {
- return PRINCIPAL_AXES;
- }
- else if( s == "Kurtosis" )
- {
- return KURTOSIS;
- }
- else if( s == "Skewness" )
- {
- return SKEWNESS;
- }
- else if( s == "Elongation" )
- {
- return ELONGATION;
- }
- else if( s == "Histogram" )
- {
- return HISTOGRAM;
- }
- // can't recognize the namespace
- return Superclass::GetAttributeFromName( s );
- }
-
- static std::string GetNameFromAttribute( const AttributeType & a )
- {
- switch( a )
- {
- case MINIMUM:
- return "Minimum";
- break;
- case MAXIMUM:
- return "Maximum";
- break;
- case MEAN:
- return "Mean";
- break;
- case SUM:
- return "Sum";
- break;
- case SIGMA:
- return "Sigma";
- break;
- case VARIANCE:
- return "Variance";
- break;
- case MEDIAN:
- return "Median";
- break;
- case MAXIMUM_INDEX:
- return "MaximumIndex";
- break;
- case MINIMUM_INDEX:
- return "MinimumIndex";
- break;
- case CENTER_OF_GRAVITY:
- return "CenterOfGravity";
- break;
-/* case CENTRAL_MOMENTS:
- return "CentralMoments";
- break;*/
- case PRINCIPAL_MOMENTS:
- return "PrincipalMoments";
- break;
- case PRINCIPAL_AXES:
- return "PrincipalAxes";
- break;
- case KURTOSIS:
- return "Kurtosis";
- break;
- case SKEWNESS:
- return "Skewness";
- break;
- case ELONGATION:
- return "Elongation";
- break;
- case HISTOGRAM:
- return "Histogram";
- break;
- }
- // can't recognize the namespace
- return Superclass::GetNameFromAttribute( a );
- }
-
- typedef ImageRegion< ImageDimension > RegionType;
-
- typedef typename Superclass::CentroidType CentroidType;
-
-
- virtual void CopyAttributesFrom( const Self * src )
- {
- Superclass::CopyAttributesFrom( src );
-
- m_Minimum = src->m_Minimum;
- m_Maximum = src->m_Maximum;
- m_Mean = src->m_Mean;
- m_Sum = src->m_Sum;
- m_Sigma = src->m_Sigma;
- m_Variance = src->m_Variance;
- m_Median = src->m_Median;
- m_MaximumIndex = src->m_MaximumIndex;
- m_MinimumIndex = src->m_MinimumIndex;
- m_CenterOfGravity = src->m_CenterOfGravity;
-// m_CentralMoments = src->m_CentralMoments;
- m_PrincipalMoments = src->m_PrincipalMoments;
- m_PrincipalAxes = src->m_PrincipalAxes;
- m_Kurtosis = src->m_Kurtosis;
- m_Skewness = src->m_Skewness;
- m_Elongation = src->m_Elongation;
- m_Histogram = src->m_Histogram;
- }
-
-// itkGetConstMacro( Minimum, double );
-// itkSetMacro( Minimum, double );
- const double & GetMinimum() const
- {
- return m_Minimum;
- }
-
- void SetMinimum( const double & v )
- {
- m_Minimum = v;
- }
-
-// itkGetConstMacro( Maximum, double );
-// itkSetMacro( Maximum, double );
- const double & GetMaximum() const
- {
- return m_Maximum;
- }
-
- void SetMaximum( const double & v )
- {
- m_Maximum = v;
- }
-
-// itkGetConstMacro( Mean, double );
-// itkSetMacro( Mean, double );
- const double & GetMean() const
- {
- return m_Mean;
- }
-
- void SetMean( const double & v )
- {
- m_Mean = v;
- }
-
-// itkGetConstMacro( Sum, double );
-// itkSetMacro( Sum, double );
- const double & GetSum() const
- {
- return m_Sum;
- }
-
- void SetSum( const double & v )
- {
- m_Sum = v;
- }
-
-// itkGetConstMacro( Sigma, double );
-// itkSetMacro( Sigma, double );
- const double & GetSigma() const
- {
- return m_Sigma;
- }
-
- void SetSigma( const double & v )
- {
- m_Sigma = v;
- }
-
-// itkGetConstMacro( Variance, double );
-// itkSetMacro( Variance, double );
- const double & GetVariance() const
- {
- return m_Variance;
- }
-
- void SetVariance( const double & v )
- {
- m_Variance = v;
- }
-
-// itkGetConstMacro( Median, double );
-// itkSetMacro( Median, double );
- const double & GetMedian() const
- {
- return m_Median;
- }
-
- void SetMedian( const double & v )
- {
- m_Median = v;
- }
-
-// itkGetConstMacro( MaximumIndex, IndexType );
-// itkSetMacro( MaximumIndex, IndexType );
- const IndexType & GetMaximumIndex() const
- {
- return m_MaximumIndex;
- }
-
- void SetMaximumIndex( const IndexType & v )
- {
- m_MaximumIndex = v;
- }
-
-// itkGetConstMacro( MinimumIndex, IndexType );
-// itkSetMacro( MinimumIndex, IndexType );
- const IndexType & GetMinimumIndex() const
- {
- return m_MinimumIndex;
- }
-
- void SetMinimumIndex( const IndexType & v )
- {
- m_MinimumIndex = v;
- }
-
-// itkGetConstMacro( CenterOfGravity, PointType );
-// itkSetMacro( CenterOfGravity, PointType );
- const PointType & GetCenterOfGravity() const
- {
- return m_CenterOfGravity;
- }
-
- void SetCenterOfGravity( const PointType & v )
- {
- m_CenterOfGravity = v;
- }
-
-// itkGetConstMacro( CentralMoments, MatrixType );
-// itkSetMacro( CentralMoments, MatrixType );
-/* const MatrixType & GetCentralMoments() const
- {
- return m_CentralMoments;
- }
-
- void SetCentralMoments( const MatrixType & v )
- {
- m_CentralMoments = v;
- }*/
-
-// itkGetConstMacro( PrincipalMoments, VectorType );
-// itkSetMacro( PrincipalMoments, VectorType );
- const VectorType & GetPrincipalMoments() const
- {
- return m_PrincipalMoments;
- }
-
- void SetPrincipalMoments( const VectorType & v )
- {
- m_PrincipalMoments = v;
- }
-
-// itkGetConstMacro( PrincipalAxes, MatrixType );
-// itkSetMacro( PrincipalAxes, MatrixType );
- const MatrixType & GetPrincipalAxes() const
- {
- return m_PrincipalAxes;
- }
-
- void SetPrincipalAxes( const MatrixType & v )
- {
- m_PrincipalAxes = v;
- }
-
-// itkGetConstMacro( Skewness, double );
-// itkSetMacro( Skewness, double );
- const double & GetSkewness() const
- {
- return m_Skewness;
- }
-
- void SetSkewness( const double & v )
- {
- m_Skewness = v;
- }
-
-// itkGetConstMacro( Kurtosis, double );
-// itkSetMacro( Kurtosis, double );
- const double & GetKurtosis() const
- {
- return m_Kurtosis;
- }
-
- void SetKurtosis( const double & v )
- {
- m_Kurtosis = v;
- }
-
-// itkGetConstMacro( Elongation, double );
-// itkSetMacro( Elongation, double );
- const double & GetElongation() const
- {
- return m_Elongation;
- }
-
- void SetElongation( const double & v )
- {
- m_Elongation = v;
- }
-
-// itkGetConstMacro( Histogram, double );
-// itkSetMacro( Histogram, double );
- const HistogramType * GetHistogram() const
- {
- return m_Histogram;
- }
-
- void SetHistogram( const HistogramType * v )
- {
- m_Histogram = v;
- }
-
-
-// some helper methods - not really required, but really useful!
-
- /** Affine transform for mapping to and from principal axis */
- typedef AffineTransform<double,itkGetStaticConstMacro(ImageDimension)> AffineTransformType;
- typedef typename AffineTransformType::Pointer AffineTransformPointer;
-
- /** Get the affine transform from principal axes to physical axes
- * This method returns an affine transform which transforms from
- * the principal axes coordinate system to physical coordinates. */
- AffineTransformPointer GetPrincipalAxesToPhysicalAxesTransform() const
- {
- typename AffineTransformType::MatrixType matrix;
- typename AffineTransformType::OffsetType offset;
- for (unsigned int i = 0; i < ImageDimension; i++)
- {
- offset[i] = m_CenterOfGravity[i];
- for (unsigned int j = 0; j < ImageDimension; j++)
- {
- matrix[j][i] = m_PrincipalAxes[i][j]; // Note the transposition
- }
- }
-
- AffineTransformPointer result = AffineTransformType::New();
-
- result->SetMatrix(matrix);
- result->SetOffset(offset);
-
- return result;
- }
-
- /** Get the affine transform from physical axes to principal axes
- * This method returns an affine transform which transforms from
- * the physical coordinate system to the principal axes coordinate
- * system. */
- AffineTransformPointer GetPhysicalAxesToPrincipalAxesTransform(void) const
- {
- typename AffineTransformType::MatrixType matrix;
- typename AffineTransformType::OffsetType offset;
- for (unsigned int i = 0; i < ImageDimension; i++)
- {
- offset[i] = m_CenterOfGravity[i];
- for (unsigned int j = 0; j < ImageDimension; j++)
- {
- matrix[j][i] = m_PrincipalAxes[i][j]; // Note the transposition
- }
- }
-
- AffineTransformPointer result = AffineTransformType::New();
- result->SetMatrix(matrix);
- result->SetOffset(offset);
-
- AffineTransformPointer inverse = AffineTransformType::New();
- result->GetInverse(inverse);
-
- return inverse;
- }
-
-
-
-protected:
- StatisticsLabelObject()
- {
- m_Minimum = 0;
- m_Maximum = 0;
- m_Mean = 0;
- m_Sum = 0;
- m_Sigma = 0;
- m_Variance = 0;
- m_Median = 0;
- m_MaximumIndex.Fill(0);
- m_MinimumIndex.Fill(0);
- m_CenterOfGravity.Fill(0);
-// m_CentralMoments.Fill(0);
- m_PrincipalMoments.Fill(0);
- m_PrincipalAxes.Fill(0);
- m_Kurtosis = 0;
- m_Skewness = 0;
- m_Elongation = 0;
- m_Histogram = NULL;
- }
-
-
- void PrintSelf(std::ostream& os, Indent indent) const
- {
- Superclass::PrintSelf( os, indent );
-
- os << indent << "Minimum: " << m_Minimum << std::endl;
- os << indent << "Maximum: " << m_Maximum << std::endl;
- os << indent << "Mean: " << m_Mean << std::endl;
- os << indent << "Sum: " << m_Sum << std::endl;
- os << indent << "Sigma: " << m_Sigma << std::endl;
- os << indent << "Variance: " << m_Variance << std::endl;
- os << indent << "Median: " << m_Median << std::endl;
- os << indent << "MaximumIndex: " << m_MaximumIndex << std::endl;
- os << indent << "MinimumIndex: " << m_MinimumIndex << std::endl;
- os << indent << "CenterOfGravity: " << m_CenterOfGravity << std::endl;
-// os << indent << "CentralMoments: " << std::endl << m_CentralMoments;
- os << indent << "PrincipalMoments: " << m_PrincipalMoments << std::endl;
- os << indent << "PrincipalAxes: " << std::endl << m_PrincipalAxes;
- os << indent << "Skewness: " << m_Skewness << std::endl;
- os << indent << "Kurtosis: " << m_Kurtosis << std::endl;
- os << indent << "Elongation: " << m_Elongation << std::endl;
- os << indent << "Histogram: ";
- if( m_Histogram )
- {
- os << "NULL" << std::endl;
- }
- else
- {
- m_Histogram->Print( os, indent );
- }
- }
-
-private:
- StatisticsLabelObject(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
- double m_Minimum;
- double m_Maximum;
- double m_Mean;
- double m_Sum;
- double m_Sigma;
- double m_Variance;
- double m_Median;
- IndexType m_MaximumIndex;
- IndexType m_MinimumIndex;
- PointType m_CenterOfGravity;
-// MatrixType m_CentralMoments;
- VectorType m_PrincipalMoments;
- MatrixType m_PrincipalAxes;
- double m_Skewness;
- double m_Kurtosis;
- double m_Elongation;
- typename HistogramType::ConstPointer m_Histogram;
-
-};
-
-} // end namespace itk
-
-#endif
diff --git a/Utilities/InsightJournal/itkStatisticsOpeningLabelMapFilter.h b/Utilities/InsightJournal/itkStatisticsOpeningLabelMapFilter.h
deleted file mode 100644
index 24960ff7eccf2b8592a120f7f7368bae2118eecc..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkStatisticsOpeningLabelMapFilter.h
+++ /dev/null
@@ -1,104 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkStatisticsOpeningLabelMapFilter.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 __itkStatisticsOpeningLabelMapFilter_h
-#define __itkStatisticsOpeningLabelMapFilter_h
-
-#include "itkShapeOpeningLabelMapFilter.h"
-#include "itkStatisticsLabelObject.h"
-
-namespace itk {
-/** \class StatisticsOpeningLabelMapFilter
- * \brief remove the objects according to the value of their statistics attribute
- *
- * StatisticsOpeningLabelMapFilter removes the objects in a lavbel collection 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, BinaryStatisticsOpeningImageFilter, LabelShapeOpeningImageFilter
- * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
- */
-template<class TImage>
-class ITK_EXPORT StatisticsOpeningLabelMapFilter :
- public ShapeOpeningLabelMapFilter<TImage>
-{
-public:
- /** Standard class typedefs. */
- typedef StatisticsOpeningLabelMapFilter Self;
- typedef ShapeOpeningLabelMapFilter<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 typename LabelObjectType::AttributeType AttributeType;
-
- /** ImageDimension constants */
- itkStaticConstMacro(ImageDimension, unsigned int,
- TImage::ImageDimension);
-
- /** Standard New method. */
- itkNewMacro(Self);
-
- /** Runtime information support. */
- itkTypeMacro(StatisticsOpeningLabelMapFilter,
- ShapeOpeningLabelMapFilter);
-
-#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
-
-
-
-protected:
- StatisticsOpeningLabelMapFilter();
- ~StatisticsOpeningLabelMapFilter() {};
-
- void GenerateData();
-
- template <class TAttributeAccessor> void TemplatedGenerateData();
-
-private:
- StatisticsOpeningLabelMapFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
-} ; // end of class
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkStatisticsOpeningLabelMapFilter.txx"
-#endif
-
-#endif
-
-
diff --git a/Utilities/InsightJournal/itkStatisticsOpeningLabelMapFilter.txx b/Utilities/InsightJournal/itkStatisticsOpeningLabelMapFilter.txx
deleted file mode 100644
index d5efa85e04aad69254d468f9f48d760fe7fd571d..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkStatisticsOpeningLabelMapFilter.txx
+++ /dev/null
@@ -1,118 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkStatisticsOpeningLabelMapFilter.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 __itkStatisticsOpeningLabelMapFilter_txx
-#define __itkStatisticsOpeningLabelMapFilter_txx
-
-#include "itkStatisticsOpeningLabelMapFilter.h"
-#include "itkProgressReporter.h"
-
-
-namespace itk {
-
-template <class TImage>
-StatisticsOpeningLabelMapFilter<TImage>
-::StatisticsOpeningLabelMapFilter()
-{
- this->m_Attribute = LabelObjectType::MEAN;
-}
-
-
-template <class TImage>
-void
-StatisticsOpeningLabelMapFilter<TImage>
-::GenerateData()
-{
- switch( this->m_Attribute )
- {
- case LabelObjectType::MINIMUM:
- TemplatedGenerateData< typename Functor::MinimumLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::MAXIMUM:
- TemplatedGenerateData< typename Functor::MaximumLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::MEAN:
- TemplatedGenerateData< typename Functor::MeanLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::SUM:
- TemplatedGenerateData< typename Functor::SumLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::SIGMA:
- TemplatedGenerateData< typename Functor::SigmaLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::VARIANCE:
- TemplatedGenerateData< typename Functor::VarianceLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::MEDIAN:
- TemplatedGenerateData< typename Functor::MedianLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::KURTOSIS:
- TemplatedGenerateData< typename Functor::KurtosisLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::SKEWNESS:
- TemplatedGenerateData< typename Functor::SkewnessLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::ELONGATION:
- TemplatedGenerateData< typename Functor::ElongationLabelObjectAccessor< LabelObjectType > >();
- break;
- default:
- Superclass::GenerateData();
- break;
- }
-}
-
-template <class TImage>
-template <class TAttributeAccessor>
-void
-StatisticsOpeningLabelMapFilter<TImage>
-::TemplatedGenerateData()
-{
- // Allocate the output
- this->AllocateOutputs();
-
- ImageType * output = this->GetOutput();
-
- TAttributeAccessor 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;
-
- if( ( !this->m_ReverseOrdering && accessor( labelObject ) < this->m_Lambda )
- || ( this->m_ReverseOrdering && accessor( labelObject ) > this->m_Lambda ) )
- {
- // must increment the iterator before removing the object to avoid invalidating the iterator
- it++;
- output->RemoveLabel( label );
- }
- else
- {
- it++;
- }
-
- progress.CompletedPixel();
- }
-}
-
-}// end namespace itk
-#endif
diff --git a/Utilities/InsightJournal/itkStatisticsRelabelImageFilter.h b/Utilities/InsightJournal/itkStatisticsRelabelImageFilter.h
deleted file mode 100644
index 34b0ce0befba6d7b55ce6a015c7cc24186979a62..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkStatisticsRelabelImageFilter.h
+++ /dev/null
@@ -1,191 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkStatisticsRelabelImageFilter.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 __itkStatisticsRelabelImageFilter_h
-#define __itkStatisticsRelabelImageFilter_h
-
-#include "itkImageToImageFilter.h"
-#include "itkStatisticsLabelObject.h"
-#include "itkLabelMap.h"
-#include "itkLabelImageToLabelMapFilter.h"
-#include "itkStatisticsLabelMapFilter.h"
-#include "itkStatisticsRelabelLabelMapFilter.h"
-#include "itkLabelMapToLabelImageFilter.h"
-
-
-namespace itk {
-
-/** \class StatisticsRelabelImageFilter
- * \brief relabel objects according to their shape attributes
- *
- * StatisticsRelabelImageFilter relabel a labeled image according to the statistics attributes 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 StatisticsLabelObject, RelabelComponentImageFilter
- * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
- */
-template<class TInputImage, class TFeatureImage>
-class ITK_EXPORT StatisticsRelabelImageFilter :
- public ImageToImageFilter<TInputImage, TInputImage>
-{
-public:
- /** Standard class typedefs. */
- typedef StatisticsRelabelImageFilter 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<InputImagePixelType, ImageDimension> LabelObjectType;
- typedef typename itk::LabelMap< LabelObjectType > LabelMapType;
- typedef typename itk::LabelImageToLabelMapFilter< InputImageType, LabelMapType > LabelizerType;
- typedef typename itk::StatisticsLabelMapFilter< LabelMapType, TFeatureImage > LabelObjectValuatorType;
- typedef typename LabelObjectType::AttributeType AttributeType;
- typedef typename itk::StatisticsRelabelLabelMapFilter< LabelMapType > RelabelType;
- typedef typename itk::LabelMapToLabelImageFilter< LabelMapType, OutputImageType > BinarizerType;
-
- /** Standard New method. */
- itkNewMacro(Self);
-
- /** Runtime information support. */
- itkTypeMacro(StatisticsRelabelImageFilter,
- 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 );
-
- /**
- * Set/Get the attribute to use. 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:
- StatisticsRelabelImageFilter();
- ~StatisticsRelabelImageFilter() {};
- void PrintSelf(std::ostream& os, Indent indent) const;
-
- /** StatisticsRelabelImageFilter needs the entire input be
- * available. Thus, it needs to provide an implementation of
- * GenerateInputRequestedRegion(). */
- void GenerateInputRequestedRegion() ;
-
- /** StatisticsRelabelImageFilter will produce the entire output. */
- void EnlargeOutputRequestedRegion(DataObject *itkNotUsed(output));
-
- /** Single-threaded version of GenerateData. This filter delegates
- * to GrayscaleGeodesicErodeImageFilter. */
- void GenerateData();
-
-private:
- StatisticsRelabelImageFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
- OutputImagePixelType m_BackgroundValue;
- bool m_ReverseOrdering;
- AttributeType m_Attribute;
-} ; // end of class
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkStatisticsRelabelImageFilter.txx"
-#endif
-
-#endif
-
-
diff --git a/Utilities/InsightJournal/itkStatisticsRelabelImageFilter.txx b/Utilities/InsightJournal/itkStatisticsRelabelImageFilter.txx
deleted file mode 100644
index 7fb471ab73b2a33363d0e476c7e4f3a8fe62d3c9..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkStatisticsRelabelImageFilter.txx
+++ /dev/null
@@ -1,128 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkStatisticsRelabelImageFilter.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 __itkStatisticsRelabelImageFilter_txx
-#define __itkStatisticsRelabelImageFilter_txx
-
-#include "itkStatisticsRelabelImageFilter.h"
-#include "itkProgressAccumulator.h"
-
-
-namespace itk {
-
-template<class TInputImage, class TFeatureImage>
-StatisticsRelabelImageFilter<TInputImage, TFeatureImage>
-::StatisticsRelabelImageFilter()
-{
- m_BackgroundValue = NumericTraits<OutputImagePixelType>::NonpositiveMin();
- m_ReverseOrdering = false;
- m_Attribute = LabelObjectType::MEAN;
- this->SetNumberOfRequiredInputs(2);
-}
-
-template<class TInputImage, class TFeatureImage>
-void
-StatisticsRelabelImageFilter<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
-StatisticsRelabelImageFilter<TInputImage, TFeatureImage>
-::EnlargeOutputRequestedRegion(DataObject *)
-{
- this->GetOutput()
- ->SetRequestedRegion( this->GetOutput()->GetLargestPossibleRegion() );
-}
-
-
-template<class TInputImage, class TFeatureImage>
-void
-StatisticsRelabelImageFilter<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->SetBackgroundValue( m_BackgroundValue );
- labelizer->SetNumberOfThreads( this->GetNumberOfThreads() );
- progress->RegisterInternalFilter(labelizer, .3f);
-
- typename LabelObjectValuatorType::Pointer valuator = LabelObjectValuatorType::New();
- valuator->SetInput( labelizer->GetOutput() );
- valuator->SetFeatureImage( this->GetFeatureImage() );
- valuator->SetLabelImage( this->GetInput() );
- 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 RelabelType::Pointer opening = RelabelType::New();
- opening->SetInput( valuator->GetOutput() );
- 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->SetNumberOfThreads( this->GetNumberOfThreads() );
- progress->RegisterInternalFilter(binarizer, .2f);
-
- binarizer->GraftOutput( this->GetOutput() );
- binarizer->Update();
- this->GraftOutput( binarizer->GetOutput() );
-}
-
-
-template<class TInputImage, class TFeatureImage>
-void
-StatisticsRelabelImageFilter<TInputImage, TFeatureImage>
-::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;
- os << indent << "Attribute: " << LabelObjectType::GetNameFromAttribute(m_Attribute) << " (" << m_Attribute << ")" << std::endl;
-}
-
-}// end namespace itk
-#endif
diff --git a/Utilities/InsightJournal/itkStatisticsRelabelLabelMapFilter.h b/Utilities/InsightJournal/itkStatisticsRelabelLabelMapFilter.h
deleted file mode 100644
index 3b92a789943f5a05efb91fed8b047d9a64f5ee21..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkStatisticsRelabelLabelMapFilter.h
+++ /dev/null
@@ -1,102 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkStatisticsRelabelLabelMapFilter.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 __itkStatisticsRelabelLabelMapFilter_h
-#define __itkStatisticsRelabelLabelMapFilter_h
-
-#include "itkShapeRelabelLabelMapFilter.h"
-#include "itkStatisticsLabelObject.h"
-
-namespace itk {
-/** \class StatisticsRelabelLabelMapFilter
- * \brief relabel objects according to their shape attributes
- *
- * StatisticsRelabelLabelMapFilter relabel a label collection image according to the statistics attributes 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 StatisticsLabelObject, RelabelComponentImageFilter
- * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
- */
-template<class TImage >
-class ITK_EXPORT StatisticsRelabelLabelMapFilter :
- public ShapeRelabelLabelMapFilter<TImage>
-{
-public:
- /** Standard class typedefs. */
- typedef StatisticsRelabelLabelMapFilter Self;
- typedef ShapeRelabelLabelMapFilter<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 typename LabelObjectType::AttributeType AttributeType;
-
- /** ImageDimension constants */
- itkStaticConstMacro(ImageDimension, unsigned int,
- TImage::ImageDimension);
-
- /** Standard New method. */
- itkNewMacro(Self);
-
- /** Runtime information support. */
- itkTypeMacro(StatisticsRelabelLabelMapFilter,
- ShapeRelabelLabelMapFilter);
-
-#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
-
-
-protected:
- StatisticsRelabelLabelMapFilter();
- ~StatisticsRelabelLabelMapFilter() {};
-
- void GenerateData();
-
- template <class TAttributeAccessor> void TemplatedGenerateData();
-
-private:
- StatisticsRelabelLabelMapFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-
-} ; // end of class
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkStatisticsRelabelLabelMapFilter.txx"
-#endif
-
-#endif
-
-
diff --git a/Utilities/InsightJournal/itkStatisticsRelabelLabelMapFilter.txx b/Utilities/InsightJournal/itkStatisticsRelabelLabelMapFilter.txx
deleted file mode 100644
index fa3ce6caeb33c6220e0d3d6a79f7b46e46b45de2..0000000000000000000000000000000000000000
--- a/Utilities/InsightJournal/itkStatisticsRelabelLabelMapFilter.txx
+++ /dev/null
@@ -1,142 +0,0 @@
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkStatisticsRelabelLabelMapFilter.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 __itkStatisticsRelabelLabelMapFilter_txx
-#define __itkStatisticsRelabelLabelMapFilter_txx
-
-#include "itkStatisticsRelabelLabelMapFilter.h"
-#include "itkProgressReporter.h"
-
-
-namespace itk {
-
-template <class TImage>
-StatisticsRelabelLabelMapFilter<TImage>
-::StatisticsRelabelLabelMapFilter()
-{
- this->m_Attribute = LabelObjectType::MEAN;
-}
-
-
-template <class TImage>
-void
-StatisticsRelabelLabelMapFilter<TImage>
-::GenerateData()
-{
- switch( this->m_Attribute )
- {
- case LabelObjectType::MINIMUM:
- TemplatedGenerateData< typename Functor::MinimumLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::MAXIMUM:
- TemplatedGenerateData< typename Functor::MaximumLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::MEAN:
- TemplatedGenerateData< typename Functor::MeanLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::SUM:
- TemplatedGenerateData< typename Functor::SumLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::SIGMA:
- TemplatedGenerateData< typename Functor::SigmaLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::VARIANCE:
- TemplatedGenerateData< typename Functor::VarianceLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::MEDIAN:
- TemplatedGenerateData< typename Functor::MedianLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::KURTOSIS:
- TemplatedGenerateData< typename Functor::KurtosisLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::SKEWNESS:
- TemplatedGenerateData< typename Functor::SkewnessLabelObjectAccessor< LabelObjectType > >();
- break;
- case LabelObjectType::ELONGATION:
- TemplatedGenerateData< typename Functor::ElongationLabelObjectAccessor< LabelObjectType > >();
- break;
- default:
- Superclass::GenerateData();
- break;
- }
-}
-
-
-template <class TImage>
-template <class TAttributeAccessor>
-void
-StatisticsRelabelLabelMapFilter<TImage>
-::TemplatedGenerateData()
-{
- // 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( this->m_ReverseOrdering )
- {
- Functor::LabelObjectReverseComparator< LabelObjectType, TAttributeAccessor > comparator;
- std::sort( labelObjects.begin(), labelObjects.end(), comparator );
- }
- else
- {
- Functor::LabelObjectComparator< LabelObjectType, TAttributeAccessor > 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();
- }
-}
-
-}// end namespace itk
-#endif