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Commit 05c8ebc9 authored by Julien Michel's avatar Julien Michel
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Ajout du filtre de segmentation de la pyramide morphologique.

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Code/MultiScale/otbMorphologicalPyramidSegmenter.h 0 → 100644
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/*=========================================================================
Program: ORFEO Toolbox
Language: C++
Date: $Date$
Version: $Revision$
Copyright (c) Centre National d'Etudes Spatiales. All rights reserved.
See OTBCopyright.txt 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 _otbMorphologicalPyramidSegmenter_h
#define _otbMorphologicalPyramidSegmenter_h
#include "itkImageToImageFilter.h"
namespace otb
{
namespace morphologicalPyramid
{
/**
* \class Segmenter
* \brief This class performs the segmentation of a detail image extracted from a
* morphological pyramid analysis.
*
* This class performs the segmentation of a detail image extracted from a
* morphological pyramid analysis.
*
* The Segmentation is perfomed using the ConnectedThresholdImageFilter. The seeds
* are extracted from the image using the ImageToPointSetFilter. The thresolds are set
* by using quantiles computed with the HistogramGenerator.
*
* \sa MorphologicalPyramidAnalyseFilter
* \sa MorphologicalPyramidSynthesisFilter
* \sa ResampleImageFilter
* \sa LinearInterpolateImageFunction
* \sa ScaleTransform
*/
template <class TInputImage, class TOutputImage>
class Segmenter
: public itk::ImageToImageFilter<TInputImage,TOutputImage>
{
public :
/** Standard typedefs */
typedef Segmenter Self;
typedef itk::ImageToImageFilter<TInputImage,TOutputImage> Superclass;
typedef itk::SmartPointer<Self> Pointer;
typedef itk::SmartPointer<const Self> ConstPointer;
/** Creation through object factory macro */
itkNewMacro(Self);
/** Type macro */
itkTypeMacro(Segmenter,ImageToImageFilter);
/** Template parameters typedefs */
typedef TInputImage InputImageType;
typedef typename InputImageType::PixelType InputPixelType;
typedef typename InputImageType::Pointer InputImagePointerType;
typedef TOutputImage OutputImageType;
typedef typename OutputImageType::Pointer OutputImagePointerType;
typedef typename OutputImageType::PixelType OutputPixelType;
typedef typename OutputImageType::RegionType OutputImageRegionType;
typedef typename OutputImageType::SizeType SizeType;
typedef typename OutputImageType::SpacingType SpacingType;
/** ImageDimension constants */
itkStaticConstMacro(DetailsImageDimension, unsigned int,
TInputImage::ImageDimension);
itkStaticConstMacro(OriginalImageDimension, unsigned int,
TInputImage::ImageDimension);
itkStaticConstMacro(OutputImageDimension, unsigned int,
TOutputImage::ImageDimension);
/**
* Set the details image.
* \param detailsImage The details image from the morphological pyramid
*/
void SetDetailsImage(const InputImageType * detailsImage);
/**
* Set the details image.
* \return detailsImage The input details image.
*/
InputImageType * GetDetailsImage(void);
/**
* Set the original image.
* \param originalImage The original image to segment.
*/
void SetOriginalImage(const InputImageType * originalImage);
/**
* Get the original image.
* \return originalImage The original image to segment.
*/
InputImageType * GetOriginalImage(void);
/** Min object size parameter accessor */
itkSetMacro(MinimumObjectSize,unsigned long);
itkGetMacro(MinimumObjectSize,unsigned long);
itkSetMacro(SeedsQuantile,float);
itkGetMacro(SeedsQuantile,float);
itkSetMacro(ConnectedThresholdQuantile,float);
itkGetMacro(ConnectedThresholdQuantile,float);
itkSetMacro(SegmentDarkDetailsBool,bool);
itkGetMacro(SegmentDarkDetailsBool,bool);
itkBooleanMacro(SegmentDarkDetailsBool);
itkGetMacro(NumberOfObjects,OutputPixelType);
protected:
/** Constructor */
Segmenter();
/** Destructor */
~Segmenter() {};
/** Main computation method */
void GenerateData(void);
/** PrintSelf method */
void PrintSelf(std::ostream& os, itk::Indent indent) const;
/**
* Configure the input datas.
*/
void GenerateInputRequestedRegion(void);
/**
* Configure the output data.
*/
void EnlargeOutputRequestedRegion(void);
private :
Segmenter(const Self&); // purposely not implemented
void operator=(const Self&); // purposely not implemented
/** Minimum size for the segmented object */
unsigned long m_MinimumObjectSize;
/** Quantile for seeds determination */
float m_SeedsQuantile;
/** Quantile to set the connectedThresholdFilter threshold */
float m_ConnectedThresholdQuantile;
/** Set to true if the details to segment are darker than background */
bool m_SegmentDarkDetailsBool;
/** Number of segmented objects */
OutputPixelType m_NumberOfObjects;
};
} // End namespace morphologicalPyramid
}// End namespace otb
#ifndef OTB_MANUAL_INSTANTIATION
#include "otbMorphologicalPyramidSegmenter.txx"
#endif
#endif
Code/MultiScale/otbMorphologicalPyramidSegmenter.txx 0 → 100644
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/*=========================================================================
Program: ORFEO Toolbox
Language: C++
Date: $Date$
Version: $Revision$
Copyright (c) Centre National d'Etudes Spatiales. All rights reserved.
See OTBCopyright.txt 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 _otbMorphologicalPyramidSegmenter_txx
#define _otbMorphologicalPyramidSegmenter_txx
#include "otbMorphologicalPyramidSegmenter.h"
#include "otbImage.h"
#include "itkConnectedThresholdImageFilter.h"
#include "itkConnectedComponentImageFilter.h"
#include "itkRelabelComponentImageFilter.h"
#include "itkThresholdImageFilter.h"
#include "itkMultiplyImageFilter.h"
#include "itkCastImageFilter.h"
#include "itkInvertIntensityImageFilter.h"
#include "itkRescaleIntensityImageFilter.h"
#include "otbThresholdImageToPointSetFilter.h"
#include "itkScalarImageToHistogramGenerator.h"
namespace otb
{
namespace morphologicalPyramid
{
/**
* Constructor
*/
template <class TInputImage,class TOuputImage>
Segmenter<TInputImage, TOuputImage>
::Segmenter()
{
this->SetNumberOfRequiredInputs(2);
}
/**
* Set the details image.
* \param detailsImage The details image from the morphological pyramid
*/
template <class TInputImage,class TOuputImage>
void
Segmenter<TInputImage, TOuputImage>
::SetDetailsImage(const InputImageType * detailsImage)
{
this->SetNthInput(0,const_cast<TInputImage *>(detailsImage));
}
/**
* Set the details image.
* \return detailsImage The input details image.
*/
template <class TInputImage,class TOuputImage>
typename Segmenter<TInputImage, TOuputImage>::InputImageType *
Segmenter<TInputImage, TOuputImage>
::GetDetailsImage(void)
{
return const_cast<InputImageType *>(this->GetInput(0));
}
/**
* Set the original image.
* \param originalImage The original image to segment.
*/
template <class TInputImage,class TOuputImage>
void
Segmenter<TInputImage, TOuputImage>
::SetOriginalImage(const InputImageType * originalImage)
{
this->SetNthInput(1,const_cast<TInputImage *>(originalImage));
}
/**
* Get the original image.
* \return originalImage The original image to segment.
*/
template <class TInputImage,class TOuputImage>
typename Segmenter<TInputImage, TOuputImage>::InputImageType *
Segmenter<TInputImage, TOuputImage>
::GetOriginalImage(void)
{
return const_cast<InputImageType *>(this->GetInput(1));
}
/**
* Configure the input datas.
*/
template <class TInputImage,class TOuputImage>
void
Segmenter<TInputImage, TOuputImage>
::GenerateInputRequestedRegion()
{
// call the superclass' implementation of this method
Superclass::GenerateInputRequestedRegion();
// get pointers to the inputs
InputImagePointerType detailsPtr =
const_cast< InputImageType * >( this->GetInput(0) );
InputImagePointerType origPtr =
const_cast< InputImageType * >( this->GetInput(1) );
if ( !detailsPtr || !origPtr )
{
return;
}
// We need to
// configure the inputs such that all the data is available.
detailsPtr->SetRequestedRegion(detailsPtr->GetLargestPossibleRegion());
origPtr->SetRequestedRegion(origPtr->GetLargestPossibleRegion());
}
/**
* Configure the output data
*/
template <class TInputImage,class TOuputImage>
void
Segmenter<TInputImage, TOuputImage>
::EnlargeOutputRequestedRegion(void)
{
this->GetOutput()
->SetRequestedRegion( this->GetOutput()->GetLargestPossibleRegion() );
}
/**
* Main computation method
*/
template <class TInputImage,class TOuputImage>
void
Segmenter<TInputImage, TOuputImage>
::GenerateData()
{
// Input images pointers
InputImagePointerType details = this->GetDetailsImage();
InputImagePointerType original = this->GetOriginalImage();
// Typedefs for details image enhancement
typedef float FloatPixelType;
typedef otb::Image<FloatPixelType,InputImageType::ImageDimension> FloatImageType;
typedef itk::InvertIntensityImageFilter<InputImageType,InputImageType> InvertFilterType;
typedef itk::MultiplyImageFilter<FloatImageType,FloatImageType,FloatImageType> MultiplyFilterType;
typedef itk::CastImageFilter<InputImageType,FloatImageType> CastImageFilterType;
typedef itk::RescaleIntensityImageFilter<FloatImageType,InputImageType> RescaleFilterType;
//Typedefs for seeds extraction
typedef itk::PointSet<InputPixelType,InputImageType::ImageDimension> PointSetType;
typedef otb::ThresholdImageToPointSetFilter<InputImageType,PointSetType> PointSetFilterType;
typedef typename PointSetType::PointsContainer::Iterator PointSetIteratorType;
typedef typename PointSetType::PointType PointType;
// Typedefs for segmentation
typedef itk::ConnectedThresholdImageFilter<InputImageType,InputImageType> ConnectedFilterType;
typedef itk::ConnectedComponentImageFilter<InputImageType,OutputImageType> LabelFilterType;
typedef itk::RelabelComponentImageFilter<OutputImageType,OutputImageType> RelabelFilterType;
typedef itk::ThresholdImageFilter<OutputImageType> ThresholdFilterType;
// Typedefs for statistics computation
typedef itk::Statistics::ScalarImageToHistogramGenerator<InputImageType> HistGeneratorType;
typedef typename HistGeneratorType::HistogramType HistogramType;
/////////////////////////////////////
//// Details image enhancement //////
/////////////////////////////////////
// Filters instantiation
typename InvertFilterType::Pointer invert;
typename CastImageFilterType::Pointer cast1 = CastImageFilterType::New();
typename CastImageFilterType::Pointer cast2 = CastImageFilterType::New();
typename MultiplyFilterType::Pointer mult = MultiplyFilterType::New();
typename RescaleFilterType::Pointer rescaler = RescaleFilterType::New();
// Pipeline connection
cast1->SetInput(details);
// If we want to segment darker detail, the original image must have its itensity inverted
if(m_SegmentDarkDetailsBool)
{
invert = InvertFilterType::New();
invert->SetInput(original);
cast2->SetInput(invert->GetOutput());
}
else
{
cast2->SetInput(original);
}
mult->SetInput1(cast1->GetOutput());
mult->SetInput2(cast2->GetOutput());
rescaler->SetInput(mult->GetOutput());
rescaler->SetOutputMinimum(0);
rescaler->SetOutputMaximum(255);
rescaler->Update();
/////////////////////////////////////
//// Thresholds computation /////////
/////////////////////////////////////
// Filter instantiation
typename HistGeneratorType::Pointer histogram = HistGeneratorType::New();
// Thresholds are computed from the quantile
histogram->SetInput(rescaler->GetOutput());
histogram->SetNumberOfBins(255);
histogram->SetMarginalScale(10.0);
histogram->Compute();
InputPixelType pointSetThreshold =
static_cast<InputPixelType>(histogram->GetOutput()->Quantile(0,m_SeedsQuantile));
InputPixelType connectedThresholdValue =
static_cast<InputPixelType>(histogram->GetOutput()->Quantile(0,m_ConnectedThresholdQuantile));
/////////////////////////////////////
//// Seeds extraction ///////////////
/////////////////////////////////////
typename PointSetFilterType::Pointer pointSetFilter = PointSetFilterType::New();
pointSetFilter->SetInput(0,details);
pointSetFilter->SetThreshold(pointSetThreshold);
pointSetFilter->Update();
/////////////////////////////////////
//// Segmentation ///////////////////
/////////////////////////////////////
// Filters instantiation
typename ConnectedFilterType::Pointer connectedThreshold = ConnectedFilterType::New();
typename LabelFilterType::Pointer labeler = LabelFilterType::New();
typename RelabelFilterType::Pointer relabeler = RelabelFilterType::New();
typename ThresholdFilterType::Pointer threshold = ThresholdFilterType::New();
//Passing seeds to the connected filter
connectedThreshold = ConnectedFilterType::New();
connectedThreshold->ClearSeeds();
connectedThreshold->SetInput(rescaler->GetOutput());
PointSetIteratorType it = pointSetFilter->GetOutput()->GetPoints()->Begin();
while(it!=pointSetFilter->GetOutput()->GetPoints()->End())
{
typename OutputImageType::IndexType index;
index[0]=static_cast<long int>(it.Value()[0]*(rescaler->GetOutput()->GetSpacing()[0]));
index[1]=static_cast<long int>(it.Value()[1]*(rescaler->GetOutput()->GetSpacing()[1]));
connectedThreshold->AddSeed(index);
it++;
}
// segmentation
connectedThreshold->SetLower(connectedThresholdValue);
// labelling
labeler = LabelFilterType::New();
relabeler = RelabelFilterType::New();
labeler->SetInput(connectedThreshold->GetOutput());
relabeler->SetInput(labeler->GetOutput());
relabeler->SetMinimumObjectSize(m_MinimumObjectSize);
relabeler->Update();
// In some cases it might happen that the whole extent of the image is segmented as a single region.
// Since this is not desirable, we test this case here to avoid it.
threshold = ThresholdFilterType::New();
threshold->SetInput(relabeler->GetOutput());
OutputPixelType num = 0;
if(relabeler->GetNumberOfObjects()==1)
{
int surface = rescaler->GetOutput()->GetLargestPossibleRegion().GetSize()[0]
*rescaler->GetOutput()->GetLargestPossibleRegion().GetSize()[1];
if(relabeler->GetSizeOfObjectsInPixels()[0]==surface)
{
num = 0;
}
else
{
num=1;
}
}
else
{
num= static_cast<OutputPixelType>(relabeler->GetNumberOfObjects());
}
threshold->ThresholdOutside(0,num);
// Output connection
threshold->GraftOutput(this->GetOutput());
threshold->Update();
this->GraftOutput(threshold->GetOutput());
m_NumberOfObjects = num;
}
/**
* PrintSelf method
*/
template <class TInputImage,class TOuputImage>
void
Segmenter<TInputImage, TOuputImage>
::PrintSelf(std::ostream& os, itk::Indent indent) const
{
Superclass::PrintSelf(os,indent);
}
} // End namespace morphologicalPyramid
} // End namespace otb
#endif
Testing/Code/MultiScale/CMakeLists.txt
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...@@ -95,6 +95,39 @@ ADD_TEST(msTvMorphoPyrMRToMSConverter ${MULTISCALE_TESTS} ...@@ -95,6 +95,39 @@ ADD_TEST(msTvMorphoPyrMRToMSConverter ${MULTISCALE_TESTS}
4 4
2.0) 2.0)
# ------- otb::MorphologicalPyramidSegmenter ----------
ADD_TEST(msTuMorphoPyrSegmenterNew ${MULTISCALE_TESTS}
otbMorphologicalPyramidSegmenterNew)
ADD_TEST(msTvMorphoPyrSegmentBright ${MULTISCALE_TESTS}
--compare-image ${TOL}
${BASELINE}/msPyrSegmenter_IKO_Halles_4_2_sf.tif
${TEMP}/msPyrSegmenter_IKO_Halles_4_2_sf.tif
otbMorphologicalPyramidSegmenter
${TEMP}/msPyrMRToMS_IKO_Halles_4_2_sf_full.tif
${INPUTDATA}/ROI_IKO_PAN_LesHalles.tif
${TEMP}/msPyrSegmenter_IKO_Halles_4_2_sf.tif
0
0.9
0.9
10
)
ADD_TEST(msTvMorphoPyrSegmentDark ${MULTISCALE_TESTS}
--compare-image ${TOL}
${BASELINE}/msPyrSegmenter_IKO_Halles_4_2_if.tif
${TEMP}/msPyrSegmenter_IKO_Halles_4_2_if.tif
otbMorphologicalPyramidSegmenter
${TEMP}/msPyrMRToMS_IKO_Halles_4_2_if_full.tif
${INPUTDATA}/ROI_IKO_PAN_LesHalles.tif
${TEMP}/msPyrSegmenter_IKO_Halles_4_2_if.tif
1
0.9
0.9
10
)
# ------- Fichiers sources CXX ----------------------------------- # ------- Fichiers sources CXX -----------------------------------
SET(BasicMultiScale_SRCS SET(BasicMultiScale_SRCS
otbMorphologicalPyramidResamplerNew.cxx otbMorphologicalPyramidResamplerNew.cxx
...@@ -105,6 +138,8 @@ otbMorphologicalPyramidSynthesisFilterNew.cxx ...@@ -105,6 +138,8 @@ otbMorphologicalPyramidSynthesisFilterNew.cxx
otbMorphologicalPyramidSynthesisFilter.cxx otbMorphologicalPyramidSynthesisFilter.cxx
otbMorphologicalPyramidMRToMSConverterNew.cxx otbMorphologicalPyramidMRToMSConverterNew.cxx
otbMorphologicalPyramidMRToMSConverter.cxx otbMorphologicalPyramidMRToMSConverter.cxx
otbMorphologicalPyramidSegmenterNew.cxx
otbMorphologicalPyramidSegmenter.cxx
) )
......
Testing/Code/MultiScale/otbMorphologicalPyramidSegmenter.cxx 0 → 100644
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/*=========================================================================
Program: ORFEO Toolbox
Language: C++
Date: $Date$
Version: $Revision$
Copyright (c) Centre National d'Etudes Spatiales. All rights reserved.
See OTBCopyright.txt 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.
=========================================================================*/
#include "itkExceptionObject.h"
#include "otbMorphologicalPyramidSegmenter.h"
#include "otbImageFileReader.h"
#include "otbImageFileWriter.h"
#include "otbImage.h"
int otbMorphologicalPyramidSegmenter(int argc, char * argv[])
{
try
{
const char* inputFilename = argv[1];
const char* originalFilename = argv[2];
const char* outputFilename1 = argv[3];
const bool segmentDark = atoi(argv[4]);
const float seedsQuantile = atof(argv[5]);
const float segmentationQuantile = atof(argv[6]);
const unsigned int minObjectSize = atoi(argv[7]);
const unsigned int Dimension = 2;
typedef unsigned char InputPixelType;
typedef unsigned short OutputPixelType;
typedef otb::Image<InputPixelType,Dimension> InputImageType;
typedef otb::Image<OutputPixelType,Dimension> OutputImageType;
typedef otb::ImageFileReader<InputImageType> ReaderType;
typedef otb::ImageFileWriter<OutputImageType> WriterType;
typedef otb::morphologicalPyramid::Segmenter<InputImageType,OutputImageType>
SegmenterType;
// Input images reading
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName(inputFilename);
ReaderType::Pointer reader2 = ReaderType::New();
reader2->SetFileName(originalFilename);
// Instantiation
SegmenterType::Pointer segmenter = SegmenterType::New();
segmenter->SetDetailsImage(reader->GetOutput());
segmenter->SetOriginalImage(reader2->GetOutput());
segmenter->SetSegmentDarkDetailsBool(segmentDark);
segmenter->SetSeedsQuantile(seedsQuantile);
segmenter->SetConnectedThresholdQuantile(segmentationQuantile);
segmenter->SetMinimumObjectSize(minObjectSize);
// File writing
WriterType::Pointer writer = WriterType::New();
writer->SetInput(segmenter->GetOutput());
writer->SetFileName(outputFilename1);
writer->Update();
}
catch( itk::ExceptionObject & err )
{
std::cout << "Exception itk::ExceptionObject thrown !" << std::endl;
std::cout << err << std::endl;
return EXIT_FAILURE;
}
catch( ... )
{
std::cout << "Unknown exception thrown !" << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
Testing/Code/MultiScale/otbMorphologicalPyramidSegmenterNew.cxx 0 → 100644
+ 54
− 0
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/*=========================================================================
Program: ORFEO Toolbox
Language: C++
Date: $Date$
Version: $Revision$
Copyright (c) Centre National d'Etudes Spatiales. All rights reserved.
See OTBCopyright.txt 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.
=========================================================================*/
#include "itkExceptionObject.h"
#include "otbMorphologicalPyramidSegmenter.h"
#include "otbImage.h"
int otbMorphologicalPyramidSegmenterNew(int argc, char * argv[])
{
try
{
const unsigned int Dimension = 2;
typedef unsigned char InputPixelType;
typedef unsigned short OutputPixelType;
typedef otb::Image<InputPixelType,Dimension> InputImageType;
typedef otb::Image<OutputPixelType,Dimension> OutputImageType;
typedef otb::morphologicalPyramid::Segmenter<InputImageType,OutputImageType>
SegmenterType;
// Instantiation
SegmenterType::Pointer segmenter = SegmenterType::New();
}
catch( itk::ExceptionObject & err )
{
std::cout << "Exception itk::ExceptionObject thrown !" << std::endl;
std::cout << err << std::endl;
return EXIT_FAILURE;
}
catch( ... )
{
std::cout << "Unknown exception thrown !" << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
Testing/Code/MultiScale/otbMultiScaleTests.cxx
+ 2
− 0
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...@@ -34,4 +34,6 @@ REGISTER_TEST(otbMorphologicalPyramidSynthesisFilterNew); ...@@ -34,4 +34,6 @@ REGISTER_TEST(otbMorphologicalPyramidSynthesisFilterNew);
REGISTER_TEST(otbMorphologicalPyramidSynthesisFilter); REGISTER_TEST(otbMorphologicalPyramidSynthesisFilter);
REGISTER_TEST(otbMorphologicalPyramidMRToMSConverterNew); REGISTER_TEST(otbMorphologicalPyramidMRToMSConverterNew);
REGISTER_TEST(otbMorphologicalPyramidMRToMSConverter); REGISTER_TEST(otbMorphologicalPyramidMRToMSConverter);
REGISTER_TEST(otbMorphologicalPyramidSegmenterNew);
REGISTER_TEST(otbMorphologicalPyramidSegmenter);
} }
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