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Merge pull request #12 from blowekamp/AddFirstOrderTextureHistorgram
Add first order texture historgram
2 parents b0c09ce + b95a220 commit a13e986

8 files changed

+575
-5
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‎include/itkFirstOrderTextureFeaturesImageFilter.h‎

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/*=========================================================================
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*
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* Copyright Insight Software Consortium
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0.txt
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*
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*=========================================================================*/
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#ifndef itkFirstOrderTextureFeaturesImageFilter_h
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#define itkFirstOrderTextureFeaturesImageFilter_h
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#include "itkMovingHistogramImageFilter.h"
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#include "itkFirstOrderTextureHistogram.h"
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namespace itk
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{
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/**
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* \class FirstOrderTextureFeaturesImageFilter
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* \brief Compute first order statistics in a neighborhood for each
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* pixel.
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*
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* The output of this filter is a multi-component image where each
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* pixel is:
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* -# mean
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* -# minimum
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* -# maximum
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* -# variance
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* -# standard deviation (sigma)
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* -# skewness
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* -# kurtosis
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* -# entropy.
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* These first order statistics are computed based on a define
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* neighborhood or kernel such as FlatStructuringElement::Box.
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*
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* The boundary is handle by only considering the pixel in the image,
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* so that the boundary pixel have lets data to compute the
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* statistics.
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*
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* \ingroup ITKTextureFeatures
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*/
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template< class TInputImage, class TOutputImage, class TKernel >
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class ITK_TEMPLATE_EXPORT FirstOrderTextureFeaturesImageFilter:
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public MovingHistogramImageFilter< TInputImage,
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TOutputImage,
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TKernel,
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typename Function::FirstOrderTextureHistogram< typename TInputImage::PixelType,
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typename TOutputImage::PixelType > >
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{
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public:
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/** Standard class typedefs. */
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typedef FirstOrderTextureFeaturesImageFilter Self;
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typedef MovingHistogramImageFilter< TInputImage, TOutputImage, TKernel,
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typename Function::FirstOrderTextureHistogram< typename TInputImage::PixelType, typename TOutputImage::PixelType> > Superclass;
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typedef SmartPointer< Self > Pointer;
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typedef SmartPointer< const Self > ConstPointer;
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/** Standard New method. */
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itkNewMacro(Self);
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/** Runtime information support. */
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itkTypeMacro(FirstOrderTextureFeaturesImageFilter,
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MovingHistogramMorphologyImageFilter);
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/** Image related typedefs. */
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typedef TInputImage InputImageType;
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typedef TOutputImage OutputImageType;
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typedef typename TInputImage::RegionType RegionType;
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typedef typename TInputImage::SizeType SizeType;
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typedef typename TInputImage::IndexType IndexType;
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typedef typename TInputImage::PixelType PixelType;
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typedef typename TInputImage::OffsetType OffsetType;
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typedef typename Superclass::OutputImageRegionType OutputImageRegionType;
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typedef typename TOutputImage::PixelType OutputPixelType;
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/** Image related typedefs. */
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itkStaticConstMacro(ImageDimension, unsigned int,
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TInputImage::ImageDimension);
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protected:
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unsigned int GetNumberOfOutputComponents() { return 8;}
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FirstOrderTextureFeaturesImageFilter()
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{
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}
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void GenerateOutputInformation()
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{
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// this methods is overloaded so that if the output image is a
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// VectorImage then the correct number of components are set.
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Superclass::GenerateOutputInformation();
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OutputImageType* output = this->GetOutput();
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if ( !output )
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{
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return;
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}
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if ( output->GetNumberOfComponentsPerPixel() != this->GetNumberOfOutputComponents() )
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{
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output->SetNumberOfComponentsPerPixel( this->GetNumberOfOutputComponents() );
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}
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}
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~FirstOrderTextureFeaturesImageFilter() {}
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private:
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FirstOrderTextureFeaturesImageFilter(const Self &); //purposely not implemented
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void operator=(const Self &); //purposely not implemented
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}; // end of class
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} // end namespace itk
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#endif

‎include/itkFirstOrderTextureHistogram.h‎

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/*=========================================================================
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*
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* Copyright Insight Software Consortium
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0.txt
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*
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*=========================================================================*/
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#ifndef itkFirstOrderTextureHistogram_h
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#define itkFirstOrderTextureHistogram_h
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#include "itkNumericTraits.h"
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#include "itkMath.h"
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#include <map>
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namespace itk
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{
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namespace Function
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{
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/* \class FirstOrderTextureHistogram
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*
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* An implementation of the "MovingHistogram" interface for the
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* MovingHistogramImageFilter class. This implementation maintains a
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* std::map based "histogram" during iteration and computes first
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* order statistics from the histogram.
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*
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* \ingroup ITKTextureFeatures
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*/
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template< class TInputPixel, class TOutputPixel >
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class ITK_TEMPLATE_EXPORT FirstOrderTextureHistogram
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{
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public:
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FirstOrderTextureHistogram()
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{
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m_Count = 0;
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}
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void AddPixel(const TInputPixel & p)
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{
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m_Map[p]++;
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++m_Count;
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}
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void RemovePixel(const TInputPixel & p)
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{
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// insert new item if one doesn't exist
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typename MapType::iterator it = m_Map.find( p );
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assert( it != m_Map.end() );
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if ( --(it->second) == 0 )
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{
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m_Map.erase( it );
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}
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--m_Count;
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}
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TOutputPixel GetValue(const TInputPixel &)
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{
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TOutputPixel out;
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NumericTraits<TOutputPixel>::SetLength( out, 8 );
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double sum = 0.0;
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double sum2 = 0.0;
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double sum3 = 0.0;
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double sum4 = 0.0;
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const size_t count = m_Count;
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double entropy = 0.0;
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size_t curCount = 0;
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for ( typename MapType::iterator i = m_Map.begin(); i != m_Map.end(); ++i )
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{
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double t = double(i->first)*double(i->second);
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sum += t;
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sum2 += ( t *= double(i->first) );
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sum3 += ( t *= double(i->first) );
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sum4 += ( t *= double(i->first) );
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curCount += i->second;
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const double p_x = double( i->second ) / count;
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entropy += -p_x*std::log( p_x ) / itk::Math::ln2;
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}
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const double mean = sum / count;
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// unbiased estimate
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const double variance = ( sum2 - ( sum * sum ) / count ) / ( count - 1 );
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const double sigma = std::sqrt(variance);
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double skewness = 0.0;
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double kurtosis = 0.0;
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if(std::abs(variance * sigma) > itk::NumericTraits<double>::min())
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{
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skewness = ( ( sum3 - 3.0 * mean * sum2 ) / count + 2.0 * mean * mean*mean ) / ( variance * sigma );
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}
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if(std::abs(variance) > itk::NumericTraits<double>::min())
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{
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kurtosis = ( sum4 / count + mean *( -4.0 * sum3 / count + mean * ( 6.0 *sum2 / count - 3.0 * mean * mean ))) /
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( variance * variance ) - 3.0;
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}
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unsigned int i = 0;
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out[i++] = mean;
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out[i++] = m_Map.begin()->first;
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out[i++] = m_Map.rbegin()->first;
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out[i++] = variance;
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out[i++] = sigma;
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out[i++] = skewness;
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out[i++] = kurtosis;
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out[i++] = entropy;
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return out;
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}
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void AddBoundary(){}
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void RemoveBoundary(){}
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private:
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typedef typename std::map< TInputPixel, size_t > MapType;
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MapType m_Map;
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size_t m_Count;
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};
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} // end namespace Function
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} // end namespace itk
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#endif

‎itk-module.cmake‎

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# By convention those modules outside of ITK are not prefixed with
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# ITK.
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if( NOT "${ITK_VERSION_MAJOR}.${ITK_VERSION_MINOR}" VERSION_LESS "4.12" )
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set(_GoogleTest_DEPENDS ITKGoogleTest)
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endif()
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# define the dependencies of the include module and the tests
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itk_module(TextureFeatures
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DEPENDS
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ITKCommon
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ITKStatistics
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ITKImageGrid
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COMPILE_DEPENDS
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ITKImageSources
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ITKMathematicalMorphology
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TEST_DEPENDS
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ITKTestKernel
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ITKMetaIO
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ITKImageIntensity
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ITKImageNoise
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${_GoogleTest_DEPENDS}
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DESCRIPTION
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"${DOCUMENTATION}"
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EXCLUDE_FROM_DEFAULT

‎test/CMakeLists.txt‎

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ScalarImageToTextureFeaturesImageFilterTestSeparateFeatures.cxx
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ScalarImageToTextureFeaturesImageFilterTestWithoutMask.cxx
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ScalarImageToTextureFeaturesImageFilterTestWithVectorImage.cxx
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ScalarImageToTextureFeaturesImageFilterTestVectorImageSeparateFeatures.cxx)
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)
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set(TextureFeaturesTests RunLengthTextureFeaturesImageFilterInstantiationTest.cxx
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RunLengthTextureFeaturesImageFilterTest.cxx
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CoocurrenceTextureFeaturesImageFilterTestSeparateFeatures.cxx
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CoocurrenceTextureFeaturesImageFilterTestWithoutMask.cxx
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CoocurrenceTextureFeaturesImageFilterTestWithVectorImage.cxx
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CoocurrenceTextureFeaturesImageFilterTestVectorImageSeparateFeatures.cxx)
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CoocurrenceTextureFeaturesImageFilterTestVectorImageSeparateFeatures.cxx
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itkFirstOrderTextureFeaturesImageFilterTest.cxx)
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CreateTestDriver(TextureFeatures "${TextureFeatures-Test_LIBRARIES}" "${TextureFeaturesTests}")
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--compare DATA{Baseline/resultSeparateFeatures_18.nrrd}
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${ITK_TEST_OUTPUT_DIR}/resultVectorImageSeparateFeatures_18.nrrd
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CoocurrenceTextureFeaturesImageFilterTestVectorImageSeparateFeatures
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DATA{Input/Scan_CBCT_13R.nrrd} DATA{Input/SegmC_CBCT_13R.nrrd} ${ITK_TEST_OUTPUT_DIR}/resultVectorImageSeparateFeatures 10 0 4200 4)
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DATA{Input/Scan_CBCT_13R.nrrd} DATA{Input/SegmC_CBCT_13R.nrrd} ${ITK_TEST_OUTPUT_DIR}/resultVectorImageSeparateFeatures 10 0 4200 4)
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itk_add_test(NAME itkFirstOrderTextureFeaturesImageFilterTest1
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COMMAND TextureFeaturesTestDriver itkFirstOrderTextureFeaturesImageFilterTest
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DATA{Input/cthead1.png}
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${ITK_TEST_OUTPUT_DIR}/itkTextureFeatureImageFilterTest1.mha
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5
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)
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if( NOT "${ITK_VERSION_MAJOR}.${ITK_VERSION_MINOR}" VERSION_LESS "4.12" )
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set(TextureFeaturesGTests
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itkFirstOrderTextureFeaturesImageFilterGTest.cxx
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)
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CreateGoogleTestDriver(TextureFeatures "${TextureFeatures-Test_LIBRARIES}" "${TextureFeaturesGTests}")
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endif()

‎test/Input/cthead1.png.md5‎

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e395391caad7463c8231bd5f2ce9d61b

‎test/Input/cthead1.png.sha512‎

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32d5c12cd02f537c901ee48ad2f438fcf5399f7292bf9c0abfb8da91b74fc2e0c4983e9650283db3462d22f05f05a8637a6c3b8188159e4bbd6dc68804a84870

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